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<title><![CDATA[The Biostar Herald for Monday, October 23, 2023]]></title>
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<div>4 days ago</div>
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<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://www.nature.com/articles/s41564-023-01426-7" rel="nofollow">Human microbiome myths and misconceptions | Nature Microbiology</a> (www.nature.com)</h3>
<blockquote><p>We hope that, by illustrating just a few examples of microbiome myths and misconceptions, we can draw increased attention to the potential problems of over-simplification and insufficient critical assessment in the microbiome literature.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41467-023-42336-w" rel="nofollow">Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement | Nature Communications</a> (www.nature.com)</h3>
<blockquote><p>Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the assembly quality at single-nucleotide resolution.</p>
</blockquote>
<p>Editor note: CRAQ ... why is this acronym so familiar, ah yes, the decade old yet still timeless Biostar post:</p>
<p>"Crac: Funny And/Or Weird Names For Bioinformatics Tools"</p>
<p><a href="https://www.biostars.org/p/67874/" rel="nofollow">Crac: Funny And/Or Weird Names For Bioinformatics Tools</a></p>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/" rel="nofollow">NCBI Datasets: Easily Access and Download Sequence Data and Metadata - NCBI Insights</a> (ncbiinsights.ncbi.nlm.nih.gov)</h3>
<blockquote><p>Effective May 2024, NCBI Datasets will replace legacy Genome and Assembly web resources</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://jlsteenwyk.com/PhyKIT/" rel="nofollow">Quick Start — phykit documentation</a> (jlsteenwyk.com)</h3>
<blockquote><p>PhyKIT, a toolkit for the UNIX shell environment with numerous functions that process multiple sequence alignments and phylogenies for broad applications</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/article/37/16/2325/6131675" rel="nofollow">https://academic.oup.com/bioinformatics/article/37/16/2325/6131675</a></h3>
<blockquote><p>We introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Sun, 22 Oct 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9578332/</guid>
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<title><![CDATA[The Biostar Herald for Monday, October 16, 2023]]></title>
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<div>11 days ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
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2.1k
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad614/7295550?login=false" rel="nofollow">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad614/7295550?login=false</a></h3>
<blockquote><p>The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/d41586-023-03238-5" rel="nofollow">ChatGPT use shows that the grant-application system is broken</a> (www.nature.com)</h3>
<blockquote><p>The fact that artificial intelligence can do much of the work makes a mockery of the process. It’s time to make it easier for scientists to ask for research funding.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/d41586-023-03177-1" rel="nofollow">Reproducibility trial: 246 biologists get different results from same data sets</a> (www.nature.com)</h3>
<blockquote><p>In a massive exercise to examine reproducibility, more than 200 biologists analysed the same sets of ecological data — and got widely divergent results. The first sweeping study1 of its kind in ecology demonstrates how much results in the field can vary, not because of differences in the environment, but because of scientists’ analytical choices</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">The microbiome field is hit and spicy. Bring it on. Last week was cancer. This week is heritability. <a href="https://t.co/poemd9Bdiz">https://t.co/poemd9Bdiz</a></p>— Seth Bordenstein (@Symbionticism) <a href="https://twitter.com/Symbionticism/status/1712272901255098596?ref_src=twsrc%5Etfw">October 12, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01669-w" rel="nofollow">Relative abundance data can misrepresent heritability of the microbiome | Microbiome | Full Text</a> (microbiomejournal.biomedcentral.com)</h3>
<blockquote><p>We derived an analytical approximation for the heritability that one obtains when using such relative, and not absolute, abundances, based on an underlying quantitative genetic model for absolute abundances. Based on this, we uncovered three problems that can arise when using relative abundances to estimate microbiome heritability: (1) the interdependency between taxa can lead to imprecise heritability estimates. This problem is most apparent for dominant taxa. (2) Large sample size leads to high false discovery rates. With enough statistical power, the result is a strong overestimation of the number of heritable taxa in a community. (3) Microbial co-abundances lead to biased heritability estimates.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8699073/" rel="nofollow">Page not available - PMC</a> (www.ncbi.nlm.nih.gov)</h3>
<blockquote><p>Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard—SNP-array based CNV calling. For nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06583-7" rel="nofollow">Unraveling the functional dark matter through global metagenomics | Nature</a> (www.nature.com)</h3>
<blockquote><p>Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.09.12.556916v1" rel="nofollow">Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. Unfortunately, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq.
To address this shortcoming, we developed Allo, a new approach to allocate multi-mapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multi-mapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multi-mapping read assignment.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.10.04.560907v1" rel="nofollow">A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific, and depends on how researchers assess the tradeoff between the quantity and quality of recovered genomes.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Our paper debunking the 2020 cancer microbiome results is now published, in <a href="https://twitter.com/mbiojournal?ref_src=twsrc%5Etfw">@mbiojournal</a>. We'll see if <a href="https://twitter.com/Nature?ref_src=twsrc%5Etfw">@nature</a> (or the authors) will retract these deeply flawed results. h/t <a href="https://twitter.com/ProfBootyPhD?ref_src=twsrc%5Etfw">@ProfBootyPhD</a> <a href="https://twitter.com/EricTopol?ref_src=twsrc%5Etfw">@EricTopol</a> <a href="https://t.co/hBvfGCvyGR">https://t.co/hBvfGCvyGR</a></p>— Steven Salzberg 💙💛 (@StevenSalzberg1) <a href="https://twitter.com/StevenSalzberg1/status/1711367878338125976?ref_src=twsrc%5Etfw">October 9, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<pubDate>Sun, 15 Oct 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9577719/</guid>
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<title><![CDATA[The Biostar Herald for Monday, October 09, 2023]]></title>
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<div class="muted">
<div>18 days ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
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2.1k
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03061-1" rel="nofollow">Genomic variant benchmark: if you cannot measure it, you cannot improve it | Genome Biology | Full Text</a> (genomebiology.biomedcentral.com)</h3>
<blockquote><p>Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. [..] In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://piscem-infer.readthedocs.io/en/latest" rel="nofollow">piscem-infer 0.3 documentation</a> (piscem-infer.readthedocs.io)</h3>
<blockquote><p>piscem-infer is a tool to perform quantification of some target (e.g. transcripts in RNA-seq, strains or species in metagenomic sequencing) using statistical inference to arrive at an abundance estimate for each target and, optionally, an associated uncertainty for each estimate.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41592-023-02026-3" rel="nofollow">Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures | Nature Methods</a> (www.nature.com)</h3>
<blockquote><p>Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that StringTie2 and bambu outperformed other tools from the six isoform detection tools tested, DESeq2, edgeR and limma-voom were best among the five differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the five tools compared, which suggests further methods development is needed for this application.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06490-x" rel="nofollow">The status of the human gene catalogue | Nature</a> (www.nature.com)</h3>
<blockquote><p>Here we review the status of the human gene catalogue and the efforts to complete it in recent years.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">We have a cool new tool (in <a href="https://twitter.com/rustlang?ref_src=twsrc%5Etfw">@rustlang</a>) for bulk seq-based quantification brewing <a href="https://t.co/msVFZl2UgR">https://t.co/msVFZl2UgR</a>. It should work well for <a href="https://twitter.com/hashtag/RNAseq?src=hash&ref_src=twsrc%5Etfw">#RNAseq</a> quant, metagenomic abundance est. & related problems. Will put up quickstart guide soon for those interested in testing. Feedback welcome!</p>— 𝕐 (@rob@genomic.social) (@nomad421) <a href="https://twitter.com/nomad421/status/1708160224257884524?ref_src=twsrc%5Etfw">September 30, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<pubDate>Sun, 08 Oct 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9577051/</guid>
<link>https://www.biostars.org/p/9577051/</link>
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<title><![CDATA[The Biostar Herald for Tuesday, September 26, 2023]]></title>
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<div>4 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
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2.1k
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/45126/" rel="nofollow">Shred</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.09.20.558707v1" rel="nofollow">GIA: A genome interval arithmetic toolkit for high performance interval set operations | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>The study introduces GIA (Genomic Interval Arithmetic) and BEDRS, a novel command-line tool and a rust library that significantly enhance the performance of genomic interval analysis. GIA outperforms existing tools like BEDOPS, BEDTools, and GenomicRanges by a factor of 2x to 20x across a range of operations.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/glarue/jgi-query" rel="nofollow">GitHub - glarue/jgi-query: A simple command-line tool to download data from Joint Genome Institute databases</a> (github.com)</h3>
<blockquote><p>A command-line tool for querying and downloading from databases hosted by the Joint Genome Institute (JGI). Useful for accessing JGI data from command-line-only resources such as remote servers, or as a lightweight alternative to JGI's other GUI-based download tools.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://link.springer.com/article/10.1186/s12859-022-05103-0" rel="nofollow">Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets | BMC Bioinformatics</a> (link.springer.com)</h3>
<blockquote><p>Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.science.org/doi/10.1126/science.adg7492" rel="nofollow">Accurate proteome-wide missense variant effect prediction with AlphaMissense</a> (www.science.org)</h3>
<p>Alphamissense is the new model developed by Deepmind to predict the effect of missense variants on proteins. Already available as a VEP plugin.</p>
<p>submitted by: <a href="https://www.biostars.org/u/45126/" rel="nofollow">Shred</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.06.23.546313v1" rel="nofollow">Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>I generated community distributions based on 12 published datasets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<pubDate>Mon, 25 Sep 2023 16:00:00 GMT</pubDate>
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<link>https://www.biostars.org/p/9575889/</link>
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<title><![CDATA[The Biostar Herald for Wednesday, September 20, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
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<div class="muted">
<div>5 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
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2.1k
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a>,
<a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/11546/" rel="nofollow">lethalfang</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://github.com/poke1024/pyalign" rel="nofollow">GitHub - poke1024/pyalign: Fast and Versatile Alignments for Python</a> (github.com)</h3>
<blockquote><p>Fast and simple alignments in Python:</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.pnas.org/doi/10.1073/pnas.2305603120" rel="nofollow">Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain</a> (www.pnas.org)</h3>
<p>Alphafold AI in action. Two disordered proteins induce specific structures when they interact with each other.</p>
<p>submitted by: <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a></p>
<hr>
<h3><a href="https://precision.fda.gov/experts/21/blog" rel="nofollow">Leveraging the Latest Technologies for Cancer Mutation Detection</a> (precision.fda.gov)</h3>
<p>Blog post by an FDA lead scientist on precisionFDA on using the latest NGS technologies for cancer mutation detection.</p>
<p>submitted by: <a href="https://www.biostars.org/u/11546/" rel="nofollow">lethalfang</a></p>
<hr>
<h3><a href="https://bioinformaticamente.com/2022/05/08/20-youtube-channels-every-bioinformatician-should-follow/amp/" rel="nofollow">40 YouTube Channels Every Bioinformatician Should Follow - BIOINFORMATICAMENTE</a> (bioinformaticamente.com)</h3>
<blockquote><p>Hi everyone. This is a very short post, actually it's a list of YouTube channels that you should follow if you are a bioinformatician or if it is your intention to pursue a career in bioinformatics.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011288" rel="nofollow">The specious art of single-cell genomics | PLOS Computational Biology</a> (journals.plos.org)</h3>
<blockquote><p>We therefore examine the practical implications of low-dimensional embedding of single-cell data and find that extensive distortions and inconsistent practices make such embeddings counter-productive for exploratory, biological analyses. In lieu of this, we discuss alternative approaches for conducting targeted embedding and feature exploration to enable hypothesis-driven biological discovery.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<pubDate>Tue, 19 Sep 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9575461/</guid>
<link>https://www.biostars.org/p/9575461/</link>
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<title><![CDATA[The Biostar Herald for Wednesday, September 06, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
<div>
<a class="" href="https://www.biostars.org/u/admin-user-1/">
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</a>
</div>
<div class="muted">
<div>7 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.1k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Check our new paper “Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation”. <a href="https://t.co/W7GYZgGbgh">https://t.co/W7GYZgGbgh</a></p>— David Kelley (@drklly) <a href="https://twitter.com/drklly/status/1698013780394041561?ref_src=twsrc%5Etfw">September 2, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">I've been coding in Python for 8 years now. ⏳<br><br>If I were to start over again in 2023, here's a roadmap:👇 <a href="https://t.co/PszcgafCUd">pic.twitter.com/PszcgafCUd</a></p>— Akshay 🚀 (@akshay_pachaar) <a href="https://twitter.com/akshay_pachaar/status/1697225233374359646?ref_src=twsrc%5Etfw">August 31, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://galantelab.github.io/sandy/" rel="nofollow">Sandy | Sandy is a bioinformatics tool that provides a simple and extensible engine to simulate single-end and paired-end reads for whole-genome and RNA sequencing.</a> (galantelab.github.io)</h3>
<blockquote><p>Sandy is a bioinformatics tool that provides a simple engine to simulate next-generation sequencing (NGS) reads for genomic and transcriptomic pipelines. Simulated data works as experimental control - a key step to optimize NGS analysis - in comparison to hypothetical models. Sandy is a straightforward, easy-to-use, fast and highly customizable tool that generates reads requiring only a fasta file as input.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Terrifying plot for those working in microbiome profiling <a href="https://t.co/8vKXX3uacW">pic.twitter.com/8vKXX3uacW</a></p>— Mick W@tson ↙️ (@BioMickWatson) <a href="https://twitter.com/BioMickWatson/status/1696488891056820452?ref_src=twsrc%5Etfw">August 29, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41598-023-40799-x" rel="nofollow">Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data | Scientific Reports</a> (www.nature.com)</h3>
<blockquote><p>We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq.[...] These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">somalier can find relatedness among thousands (or a handful if that's what you have) of samples in seconds. latest release updates a lesser-used feature to find your own sites with which to calculate kinship: <a href="https://t.co/etNxULXsk4">https://t.co/etNxULXsk4</a><br><br>thanks <a href="https://twitter.com/johanneskoester?ref_src=twsrc%5Etfw">@johanneskoester</a> for reporting!</p>— brent pedersen (@brent_p) <a href="https://twitter.com/brent_p/status/1696075088506806608?ref_src=twsrc%5Etfw">August 28, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbad107/7252269" rel="nofollow">https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbad107/7252269</a></h3>
<blockquote><p>We introduce VCFshiny, an R package that features a user-friendly web interface enabling interactive annotation, interpretation, and visualization of variant information stored in VCF files. VCFshiny offers two annotation methods, Annovar and VariantAnnotation, to add annotations such as genes or functional impact. Annotated VCF files are deemed acceptable inputs for the purpose of summarizing and visualizing variant information.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Tue, 05 Sep 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9574254/</guid>
<link>https://www.biostars.org/p/9574254/</link>
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<title><![CDATA[The Biostar Herald for Monday, August 28, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
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<img class="ui centered circular image" src="https://secure.gravatar.com/avatar/46d229b033af06a191ff2267bca9ae56?s=80&d=robohash" referrerpolicy="no-referrer">
</a>
</div>
<div class="muted">
<div>8 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.1k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad516/7251027" rel="nofollow">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad516/7251027</a></h3>
<blockquote><p>We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">A very intriguing result in the new Y chromosome paper, one that you might miss unless you read the paper closely... 1/6 <a href="https://t.co/YQt5iLIQ61">https://t.co/YQt5iLIQ61</a></p>— Steven Salzberg 💙💛 (@StevenSalzberg1) <a href="https://twitter.com/StevenSalzberg1/status/1695078983887634648?ref_src=twsrc%5Etfw">August 25, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Over 3,500 authenticated microbial genomes are currently available on the ATCC Genome Portal (<a href="https://t.co/F3UZguZ2sC">https://t.co/F3UZguZ2sC</a>) - reference genomes for 3,205 bacteria, 254 fungi, 293 viruses, and 4 protists so far. Over 100+ released every month too! :) 🧬🦠🍄🚀 <a href="https://twitter.com/hashtag/genomics?src=hash&ref_src=twsrc%5Etfw">#genomics</a> <a href="https://twitter.com/hashtag/bioinformatics?src=hash&ref_src=twsrc%5Etfw">#bioinformatics</a></p>— Jonathan Jacobs 🧬🦠🕹️🏕️ (@bioinformer) <a href="https://twitter.com/bioinformer/status/1694787161948651979?ref_src=twsrc%5Etfw">August 24, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://arxiv.org/abs/2308.07333" rel="nofollow">[2308.07333] Computational reproducibility of Jupyter notebooks from biomedical publications</a> (arxiv.org)</h3>
<blockquote><p>Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles [ ...] 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.08.21.554084v1" rel="nofollow">Flexiplex: A versatile demultiplexer and search tool for omics data | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>We developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell line specific sequences in Illumina short-read single cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools. Flexiplex is available at <a href="https://davidsongroup.github.io/flexiplex/" rel="nofollow">https://davidsongroup.github.io/flexiplex/</a>.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Sun, 27 Aug 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9573517/</guid>
<link>https://www.biostars.org/p/9573517/</link>
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<title><![CDATA[The Biostar Herald for Thursday, August 24, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
<div>
<a class="" href="https://www.biostars.org/u/admin-user-1/">
<img class="ui centered circular image" src="https://secure.gravatar.com/avatar/46d229b033af06a191ff2267bca9ae56?s=80&d=robohash" referrerpolicy="no-referrer">
</a>
</div>
<div class="muted">
<div>9 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.1k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06457-y" rel="nofollow">The complete sequence of a human Y chromosome | Nature</a> (www.nature.com)</h3>
<blockquote><p>Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Why so many names for the same contig? Isn't CM000664.2 just chr2?<br><br>Don't panic, we've got a tool for this.<br><br>fgbio CollectAlternateContigNames<a href="https://twitter.com/hashtag/Bioinformatics?src=hash&ref_src=twsrc%5Etfw">#Bioinformatics</a> <a href="https://t.co/rfjqRf7Sna">https://t.co/rfjqRf7Sna</a></p>— Nils Homer (@nilshomer) <a href="https://twitter.com/nilshomer/status/1694591605200810278?ref_src=twsrc%5Etfw">August 24, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03027-3" rel="nofollow">The CUT&RUN suspect list of problematic regions of the genome | Genome Biology | Full Text</a> (genomebiology.biomedcentral.com)</h3>
<blockquote><p>While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad480/7234613" rel="nofollow">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad480/7234613</a></h3>
<blockquote><p>In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant calling accuracy. We examine the performance of three general-purpose short-read aligners – BWA-MEM, Bowtie 2, and Arioc – in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant calling performance.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">"Data visualization is where you start and end a data analysis." -- <a href="https://twitter.com/rafalab?ref_src=twsrc%5Etfw">@rafalab</a> <a href="https://twitter.com/hashtag/JSM2023?src=hash&ref_src=twsrc%5Etfw">#JSM2023</a></p>— Stephanie Hicks (@stephaniehicks) <a href="https://twitter.com/stephaniehicks/status/1688998329256984577?ref_src=twsrc%5Etfw">August 8, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Wed, 23 Aug 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9573169/</guid>
<link>https://www.biostars.org/p/9573169/</link>
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<title><![CDATA[The Biostar Herald for Wednesday, August 09, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
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</a>
</div>
<div class="muted">
<div>11 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.1k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/50673/" rel="nofollow">manaswwm</a>,
and was edited by <a href="https://www.biostars.org/u/8494/" rel="nofollow">Ram</a>,
<a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://joss.theoj.org/papers/10.21105/joss.01762" rel="nofollow">Journal of Open Source Software: Mashtree: a rapid comparison of whole genome sequence files</a> (joss.theoj.org)</h3>
<blockquote><p>Min-hash creates distances between any two genomes, min-hash values can be used to
rapidly cluster genomes into trees using the neighbor-joining algorithm (Saitou & Nei, 1987).
We implemented this idea in software called Mashtree, which quickly and efficiently generates
large trees that would be too computationally intensive using other methods.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/vanheeringen-lab/genomepy" rel="nofollow">GitHub - vanheeringen-lab/genomepy: genes and genomes at your fingertips</a> (github.com)</h3>
<blockquote><p>genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">I think we need to talk about how devastating this cancer microbiome refutation paper from<a href="https://twitter.com/StevenSalzberg1?ref_src=twsrc%5Etfw">@StevenSalzberg1</a><br>and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/n<a href="https://t.co/wWsHTa4K8x">https://t.co/wWsHTa4K8x</a></p>— Professor Booty PhD (@ProfBootyPhD) <a href="https://twitter.com/ProfBootyPhD/status/1688386329405505536?ref_src=twsrc%5Etfw">August 7, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.07.26.550536v1" rel="nofollow">Challenges in identifying mRNA transcript starts and ends from long-read sequencing data | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Here, we systematically assess the variability and accuracy of mRNA terminal ends identified by LRS reads across multiple sequencing platforms. We find substantial inconsistencies in both the start and end coordinates of LRS reads spanning a gene, such that LRS reads often fail to accurately recapitulate annotated or empirically derived terminal ends of mRNA molecules.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06288-x" rel="nofollow">Evolution of a minimal cell | Nature</a> (www.nature.com)</h3>
<p>Evolution of a minimal version of a bacterial cell</p>
<p>submitted by: <a href="https://www.biostars.org/u/50673/" rel="nofollow">manaswwm</a></p>
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<pubDate>Tue, 08 Aug 2023 16:00:00 GMT</pubDate>
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<title><![CDATA[The Biostar Herald for Wednesday, August 02, 2023]]></title>
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<div>12 weeks ago</div>
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<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a>,
<a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/134671/" rel="nofollow">Starlitnightly</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Hey Steve, What do you think of the rebuttal - <a href="https://t.co/cv44CxCnio">https://t.co/cv44CxCnio</a></p>— Jack A Gilbert (he/him/his) (@gilbertjacka) <a href="https://twitter.com/gilbertjacka/status/1686408777007030272?ref_src=twsrc%5Etfw">August 1, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Major, fatal errors found in the data and methods of a 2020 paper in <a href="https://twitter.com/Nature?ref_src=twsrc%5Etfw">@Nature</a>, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. <a href="https://twitter.com/AbrahamGihawi?ref_src=twsrc%5Etfw">@abrahamgihawi</a> <a href="https://twitter.com/elapertea?ref_src=twsrc%5Etfw">@elapertea</a> <a href="https://twitter.com/YuchenGe1?ref_src=twsrc%5Etfw">@YuchenGe1</a> <a href="https://twitter.com/JenniferLu717?ref_src=twsrc%5Etfw">@JenniferLu717</a> <a href="https://t.co/z5Aja84kiR">https://t.co/z5Aja84kiR</a></p>— Steven Salzberg 💙💛 (@StevenSalzberg1) <a href="https://twitter.com/StevenSalzberg1/status/1686350449069244416?ref_src=twsrc%5Etfw">August 1, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.07.28.550993v1" rel="nofollow">Major data analysis errors invalidate cancer microbiome findings | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cancers [...]
Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/Starlitnightly/omicverse" rel="nofollow">GitHub - Starlitnightly/omicverse: A python library for multi omics included bulk and single cell RNA-seq analysis.</a> (github.com)</h3>
<p>OmicVerse is the fundamental package for multi omics included bulk and single cell analysis with Python. The original name of the omicverse was Pyomic, but we wanted to address a whole universe of transcriptomics, so we changed the name to OmicVerse, it aimed to solve all task in RNA-seq.</p>
<p>The OmicVerse documentation website provides an application programming interface (API) reference for each algorithm, along with tutorials describing the functionality and limitations of each algorithm and its interaction with other bulk/single-seq tools. These tutorials are also accessible through Google Colab, providing a free computing environment to support pipeline studies.</p>
<p>Our aim was to create an ecosystem for bulk/single-seq analysis and beautiful visualization within Python environments. Users can perform comprehensive transcriptome analysis using a single programming language, leveraging the machine-learning models and expertise of the Python community. As OmicVerse continues to evolve, we anticipate ongoing updates that incorporate new algorithms, features, and models. OmicVerse is expected to benefit the bulk/single-seq community by facilitating the prototyping of new models, establishing standards for the analysis of trans omics, and enhancing the scientific discovery pipeline.</p>
<p>submitted by: <a href="https://www.biostars.org/u/134671/" rel="nofollow">Starlitnightly</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.06.29.546998v1.full" rel="nofollow">Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes | bioRxiv</a> (www.biorxiv.org)</h3>
<p>Assessment of read assemblers for eukarotic genomes.</p>
<p>submitted by: <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a></p>
<hr>
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<pubDate>Tue, 01 Aug 2023 16:00:00 GMT</pubDate>
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<title><![CDATA[The Biostar Herald for Thursday, June 15, 2023]]></title>
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<div>4 months ago</div>
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<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://github.com/enormandeau/snplift" rel="nofollow">GitHub - enormandeau/snplift: Convert genetic variant coordinates across genome assemblies</a> (github.com)</h3>
<blockquote><p>SNPLift takes a tab-delimited file, for example a VCF, with locus positions from a given genome and lifts over these positions so they match a new reference genome. The goal is to rapidly leverage the availability of new genomes without having to re-align all the sample reads and then call and filter the loci again.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/sanger-pathogens/snp-sites" rel="nofollow">GitHub - sanger-pathogens/snp-sites: Finds SNP sites from a multi-FASTA alignment file</a> (github.com)</h3>
<blockquote><p>Rapidly extracts SNPs from a multi-FASTA alignment.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000949?crawler=true" rel="nofollow">From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools | Microbiology Society</a> (www.microbiologyresearch.org)</h3>
<blockquote><p>We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool–parameter–database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all ‘best’ choice.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.06.03.543588v1" rel="nofollow">miniBUSCO: a faster and more accurate reimplementation of BUSCO | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Here, we present miniBUSCO, an efficient tool for assessing the completeness of genome assemblies. miniBUSCO utilizes the protein-to-genome aligner miniprot and the datasets of conserved orthologous genes from BUSCO. Our evaluation of the real human assembly indicates that miniBUSCO achieves a 14-fold speedup over BUSCO.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://arxiv.org/abs/2306.03399" rel="nofollow">[2306.03399] Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph</a> (arxiv.org)</h3>
<blockquote><p>Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources. In this study, we present an efficient de novo assembly algorithm that combines multiple sequencing technologies to scale up population-wide telomere-to-telomere assemblies. By utilizing twenty-two human and two plant genomes, we demonstrate that our algorithm is around an order of magnitude cheaper than existing methods, while producing better diploid and haploid assemblies. Notably, our algorithm is the only feasible solution to the haplotype-resolved assembly of polyploid genomes.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Double kraken2 announcement: (a) new load of indexes at <a href="https://t.co/7RZ7nbJHye">https://t.co/7RZ7nbJHye</a>, and (b) new version v2.1.3 with bug fixes and more efficient masker <a href="https://t.co/tyqpwSwvrp">https://t.co/tyqpwSwvrp</a>. Importantly, the release also includes ... (1/2)</p>— Ben Langmead (@BenLangmead) <a href="https://twitter.com/BenLangmead/status/1666451382457495552?ref_src=twsrc%5Etfw">June 7, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Wed, 14 Jun 2023 16:00:00 GMT</pubDate>
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<title><![CDATA[The Biostar Herald for Monday, June 05, 2023]]></title>
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github-actions
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TonyRL
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Yes, I tried. The layout of the official RSS feed is not very while in some RSS reader (e.g. Miniflux). Even though you can catch fulltext to get a HTML like layout, there will be more unnecessary elements shown (e.g. entering edit mode), which are not the readers want. So I believe this route is useful for the readers.
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TonyRL
reviewed
Oct 30, 2023
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Please make it support custom tag input like /tag/transcriptome/, /tag/RNAseq/, /tag/workshop/ or /tag/transcriptomics/ instead of a single hard-coded tag only.
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Thanks for your suggestions.
I create a new PR at #13748 (comment).
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<div>4 days ago</div>
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<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/7513/" rel="nofollow">aswathyseb</a>,
<a href="https://www.biostars.org/u/45126/" rel="nofollow">Shred</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03065-x" rel="nofollow">Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates | Genome Biology | Full Text</a> (genomebiology.biomedcentral.com)</h3>
<blockquote><p>RNA velocity analysis of single cells offers the potential to predict temporal dynamics from gene expression. In many systems, RNA velocity has been observed to produce a vector field that qualitatively reflects known features of the system. However, the limitations of RNA velocity estimates are still not well understood.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad903/7331009" rel="nofollow">https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad903/7331009</a></h3>
<blockquote><p>GenBank® (<a href="https://www.ncbi.nlm.nih.gov/genbank/" rel="nofollow">https://www.ncbi.nlm.nih.gov/genbank/</a>) is a comprehensive, public database that contains 25 trillion base pairs from over 3.7 billion nucleotide sequences for 557 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. Recent updates include policies for including spatio-temporal metadata, clarified documentation for GenBank data processing, enhanced foreign contamination screening tools, new processes in the Submission Portal, migration of Entrez Genome and Assembly displays into NCBI Datasets, and the impending retirement of tbl2asn, replaced by table2asn.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Release of DeepVariant v1.6. <br><br>Support for haploid regions, chrX/Y. <br>Workflow for Pangenome FASTQ-to-VCF. <br>Major DeepTrio improvements for de novo variants. <br>Models for CompleteGenomics T7, G400<br>Add NovaSeqX to training data<br><br>Release by <a href="https://twitter.com/kishwarshafin?ref_src=twsrc%5Etfw">@kishwarshafin</a> <a href="https://t.co/ShaxqDNTfX">https://t.co/ShaxqDNTfX</a></p>— Andrew Carroll (@acarroll_ATG) <a href="https://twitter.com/acarroll_ATG/status/1717579303913721898?ref_src=twsrc%5Etfw">October 26, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/google/deepsomatic" rel="nofollow">GitHub - google/deepsomatic: DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.</a> (github.com)</h3>
<p>Google released Deepsomatic, a porting of the already well known DeepVariant, to call somatic variants from WGS from both Illumina and Pacbio, using paired tumor-normal samples.
One of the developers stated they're not planning to develop a WES model [source: <a href="https://github.com/google/deepsomatic/issues/4#issuecomment-1779657480" rel="nofollow">https://github.com/google/deepsomatic/issues/4#issuecomment-1779657480</a> ]
To date (version 1.6) no code released through Github.</p>
<p>submitted by: <a href="https://www.biostars.org/u/45126/" rel="nofollow">Shred</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">The simpleaf (simple-AF) paper by <a href="https://twitter.com/DongzeHe?ref_src=twsrc%5Etfw">@DongzeHe</a> & me was recently published in <a href="https://twitter.com/OUPBioinfo?ref_src=twsrc%5Etfw">@OUPBioinfo</a> <a href="https://t.co/8pEwSHeXoU">https://t.co/8pEwSHeXoU</a>. It describes the simpleaf tool, written in <a href="https://twitter.com/hashtag/rustlang?src=hash&ref_src=twsrc%5Etfw">#rustlang</a>, designed to track best practices & make processing <a href="https://twitter.com/hashtag/SingleCell?src=hash&ref_src=twsrc%5Etfw">#SingleCell</a> <a href="https://twitter.com/hashtag/scrna?src=hash&ref_src=twsrc%5Etfw">#scrna</a> data with alevin-fry even easier. 1/x</p>— 𝕐 (@rob@genomic.social) (@nomad421) <a href="https://twitter.com/nomad421/status/1717008740346425806?ref_src=twsrc%5Etfw">October 25, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by <a href="https://twitter.com/kishwarshafin?ref_src=twsrc%5Etfw">@kishwarshafin</a> which built off a framework by <a href="https://twitter.com/pichuan?ref_src=twsrc%5Etfw">@pichuan</a><a href="https://t.co/YpB46RlhiB">https://t.co/YpB46RlhiB</a></p>— Andrew Carroll (@acarroll_ATG) <a href="https://twitter.com/acarroll_ATG/status/1716859411887435878?ref_src=twsrc%5Etfw">October 24, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1790-4" rel="nofollow">Identifying significantly impacted pathways: a comprehensive review and assessment | Genome Biology | Full Text</a> (genomebiology.biomedcentral.com)</h3>
<blockquote><p>Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the importance of this type of analysis, more than 70 pathway analysis methods have been proposed so far. These can be categorized into two main categories: non-topology-based (non-TB) and topology-based (TB). Although some review papers discuss this topic from different aspects, there is no systematic, large-scale assessment of such methods. Furthermore, the majority of the pathway analysis approaches rely on the assumption of uniformity of p values under the null hypothesis, which is often not true.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/7513/" rel="nofollow">aswathyseb</a></p>
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<pubDate>Sun, 29 Oct 2023 16:00:00 GMT</pubDate>
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<div class="muted">
<div>11 days ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
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<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://www.nature.com/articles/s41564-023-01426-7" rel="nofollow">Human microbiome myths and misconceptions | Nature Microbiology</a> (www.nature.com)</h3>
<blockquote><p>We hope that, by illustrating just a few examples of microbiome myths and misconceptions, we can draw increased attention to the potential problems of over-simplification and insufficient critical assessment in the microbiome literature.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41467-023-42336-w" rel="nofollow">Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement | Nature Communications</a> (www.nature.com)</h3>
<blockquote><p>Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the assembly quality at single-nucleotide resolution.</p>
</blockquote>
<p>Editor note: CRAQ ... why is this acronym so familiar, ah yes, the decade old yet still timeless Biostar post:</p>
<p>"Crac: Funny And/Or Weird Names For Bioinformatics Tools"</p>
<p><a href="https://www.biostars.org/p/67874/" rel="nofollow">Crac: Funny And/Or Weird Names For Bioinformatics Tools</a></p>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2023/10/18/ncbi-datasets-access-sequence-data/" rel="nofollow">NCBI Datasets: Easily Access and Download Sequence Data and Metadata - NCBI Insights</a> (ncbiinsights.ncbi.nlm.nih.gov)</h3>
<blockquote><p>Effective May 2024, NCBI Datasets will replace legacy Genome and Assembly web resources</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://jlsteenwyk.com/PhyKIT/" rel="nofollow">Quick Start — phykit documentation</a> (jlsteenwyk.com)</h3>
<blockquote><p>PhyKIT, a toolkit for the UNIX shell environment with numerous functions that process multiple sequence alignments and phylogenies for broad applications</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/article/37/16/2325/6131675" rel="nofollow">https://academic.oup.com/bioinformatics/article/37/16/2325/6131675</a></h3>
<blockquote><p>We introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Sun, 22 Oct 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9578332/</guid>
<link>https://www.biostars.org/p/9578332/</link>
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<title><![CDATA[The Biostar Herald for Monday, October 16, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
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</div>
<div class="muted">
<div>18 days ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
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2.2k
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</div>
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad614/7295550?login=false" rel="nofollow">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad614/7295550?login=false</a></h3>
<blockquote><p>The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/d41586-023-03238-5" rel="nofollow">ChatGPT use shows that the grant-application system is broken</a> (www.nature.com)</h3>
<blockquote><p>The fact that artificial intelligence can do much of the work makes a mockery of the process. It’s time to make it easier for scientists to ask for research funding.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/d41586-023-03177-1" rel="nofollow">Reproducibility trial: 246 biologists get different results from same data sets</a> (www.nature.com)</h3>
<blockquote><p>In a massive exercise to examine reproducibility, more than 200 biologists analysed the same sets of ecological data — and got widely divergent results. The first sweeping study1 of its kind in ecology demonstrates how much results in the field can vary, not because of differences in the environment, but because of scientists’ analytical choices</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">The microbiome field is hit and spicy. Bring it on. Last week was cancer. This week is heritability. <a href="https://t.co/poemd9Bdiz">https://t.co/poemd9Bdiz</a></p>— Seth Bordenstein (@Symbionticism) <a href="https://twitter.com/Symbionticism/status/1712272901255098596?ref_src=twsrc%5Etfw">October 12, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01669-w" rel="nofollow">Relative abundance data can misrepresent heritability of the microbiome | Microbiome | Full Text</a> (microbiomejournal.biomedcentral.com)</h3>
<blockquote><p>We derived an analytical approximation for the heritability that one obtains when using such relative, and not absolute, abundances, based on an underlying quantitative genetic model for absolute abundances. Based on this, we uncovered three problems that can arise when using relative abundances to estimate microbiome heritability: (1) the interdependency between taxa can lead to imprecise heritability estimates. This problem is most apparent for dominant taxa. (2) Large sample size leads to high false discovery rates. With enough statistical power, the result is a strong overestimation of the number of heritable taxa in a community. (3) Microbial co-abundances lead to biased heritability estimates.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8699073/" rel="nofollow">Page not available - PMC</a> (www.ncbi.nlm.nih.gov)</h3>
<blockquote><p>Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard—SNP-array based CNV calling. For nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06583-7" rel="nofollow">Unraveling the functional dark matter through global metagenomics | Nature</a> (www.nature.com)</h3>
<blockquote><p>Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.09.12.556916v1" rel="nofollow">Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. Unfortunately, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq.
To address this shortcoming, we developed Allo, a new approach to allocate multi-mapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multi-mapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multi-mapping read assignment.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.10.04.560907v1" rel="nofollow">A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific, and depends on how researchers assess the tradeoff between the quantity and quality of recovered genomes.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Our paper debunking the 2020 cancer microbiome results is now published, in <a href="https://twitter.com/mbiojournal?ref_src=twsrc%5Etfw">@mbiojournal</a>. We'll see if <a href="https://twitter.com/Nature?ref_src=twsrc%5Etfw">@nature</a> (or the authors) will retract these deeply flawed results. h/t <a href="https://twitter.com/ProfBootyPhD?ref_src=twsrc%5Etfw">@ProfBootyPhD</a> <a href="https://twitter.com/EricTopol?ref_src=twsrc%5Etfw">@EricTopol</a> <a href="https://t.co/hBvfGCvyGR">https://t.co/hBvfGCvyGR</a></p>— Steven Salzberg 💙💛 (@StevenSalzberg1) <a href="https://twitter.com/StevenSalzberg1/status/1711367878338125976?ref_src=twsrc%5Etfw">October 9, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Sun, 15 Oct 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9577719/</guid>
<link>https://www.biostars.org/p/9577719/</link>
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<title><![CDATA[The Biostar Herald for Monday, October 09, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
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</a>
</div>
<div class="muted">
<div>25 days ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03061-1" rel="nofollow">Genomic variant benchmark: if you cannot measure it, you cannot improve it | Genome Biology | Full Text</a> (genomebiology.biomedcentral.com)</h3>
<blockquote><p>Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. [..] In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://piscem-infer.readthedocs.io/en/latest" rel="nofollow">piscem-infer 0.3 documentation</a> (piscem-infer.readthedocs.io)</h3>
<blockquote><p>piscem-infer is a tool to perform quantification of some target (e.g. transcripts in RNA-seq, strains or species in metagenomic sequencing) using statistical inference to arrive at an abundance estimate for each target and, optionally, an associated uncertainty for each estimate.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41592-023-02026-3" rel="nofollow">Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures | Nature Methods</a> (www.nature.com)</h3>
<blockquote><p>Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that StringTie2 and bambu outperformed other tools from the six isoform detection tools tested, DESeq2, edgeR and limma-voom were best among the five differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the five tools compared, which suggests further methods development is needed for this application.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06490-x" rel="nofollow">The status of the human gene catalogue | Nature</a> (www.nature.com)</h3>
<blockquote><p>Here we review the status of the human gene catalogue and the efforts to complete it in recent years.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">We have a cool new tool (in <a href="https://twitter.com/rustlang?ref_src=twsrc%5Etfw">@rustlang</a>) for bulk seq-based quantification brewing <a href="https://t.co/msVFZl2UgR">https://t.co/msVFZl2UgR</a>. It should work well for <a href="https://twitter.com/hashtag/RNAseq?src=hash&ref_src=twsrc%5Etfw">#RNAseq</a> quant, metagenomic abundance est. & related problems. Will put up quickstart guide soon for those interested in testing. Feedback welcome!</p>— 𝕐 (@rob@genomic.social) (@nomad421) <a href="https://twitter.com/nomad421/status/1708160224257884524?ref_src=twsrc%5Etfw">September 30, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<pubDate>Sun, 08 Oct 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9577051/</guid>
<link>https://www.biostars.org/p/9577051/</link>
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<title><![CDATA[The Biostar Herald for Tuesday, September 26, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
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<div class="muted">
<div>5 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
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2.2k
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/45126/" rel="nofollow">Shred</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.09.20.558707v1" rel="nofollow">GIA: A genome interval arithmetic toolkit for high performance interval set operations | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>The study introduces GIA (Genomic Interval Arithmetic) and BEDRS, a novel command-line tool and a rust library that significantly enhance the performance of genomic interval analysis. GIA outperforms existing tools like BEDOPS, BEDTools, and GenomicRanges by a factor of 2x to 20x across a range of operations.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/glarue/jgi-query" rel="nofollow">GitHub - glarue/jgi-query: A simple command-line tool to download data from Joint Genome Institute databases</a> (github.com)</h3>
<blockquote><p>A command-line tool for querying and downloading from databases hosted by the Joint Genome Institute (JGI). Useful for accessing JGI data from command-line-only resources such as remote servers, or as a lightweight alternative to JGI's other GUI-based download tools.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://link.springer.com/article/10.1186/s12859-022-05103-0" rel="nofollow">Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets | BMC Bioinformatics</a> (link.springer.com)</h3>
<blockquote><p>Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.science.org/doi/10.1126/science.adg7492" rel="nofollow">Accurate proteome-wide missense variant effect prediction with AlphaMissense</a> (www.science.org)</h3>
<p>Alphamissense is the new model developed by Deepmind to predict the effect of missense variants on proteins. Already available as a VEP plugin.</p>
<p>submitted by: <a href="https://www.biostars.org/u/45126/" rel="nofollow">Shred</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.06.23.546313v1" rel="nofollow">Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>I generated community distributions based on 12 published datasets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<pubDate>Mon, 25 Sep 2023 16:00:00 GMT</pubDate>
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<link>https://www.biostars.org/p/9575889/</link>
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<title><![CDATA[The Biostar Herald for Wednesday, September 20, 2023]]></title>
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</a>
</div>
<div class="muted">
<div>6 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
</div>
</div>
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a>,
<a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/11546/" rel="nofollow">lethalfang</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://github.com/poke1024/pyalign" rel="nofollow">GitHub - poke1024/pyalign: Fast and Versatile Alignments for Python</a> (github.com)</h3>
<blockquote><p>Fast and simple alignments in Python:</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.pnas.org/doi/10.1073/pnas.2305603120" rel="nofollow">Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain</a> (www.pnas.org)</h3>
<p>Alphafold AI in action. Two disordered proteins induce specific structures when they interact with each other.</p>
<p>submitted by: <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a></p>
<hr>
<h3><a href="https://precision.fda.gov/experts/21/blog" rel="nofollow">Leveraging the Latest Technologies for Cancer Mutation Detection</a> (precision.fda.gov)</h3>
<p>Blog post by an FDA lead scientist on precisionFDA on using the latest NGS technologies for cancer mutation detection.</p>
<p>submitted by: <a href="https://www.biostars.org/u/11546/" rel="nofollow">lethalfang</a></p>
<hr>
<h3><a href="https://bioinformaticamente.com/2022/05/08/20-youtube-channels-every-bioinformatician-should-follow/amp/" rel="nofollow">40 YouTube Channels Every Bioinformatician Should Follow - BIOINFORMATICAMENTE</a> (bioinformaticamente.com)</h3>
<blockquote><p>Hi everyone. This is a very short post, actually it's a list of YouTube channels that you should follow if you are a bioinformatician or if it is your intention to pursue a career in bioinformatics.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011288" rel="nofollow">The specious art of single-cell genomics | PLOS Computational Biology</a> (journals.plos.org)</h3>
<blockquote><p>We therefore examine the practical implications of low-dimensional embedding of single-cell data and find that extensive distortions and inconsistent practices make such embeddings counter-productive for exploratory, biological analyses. In lieu of this, we discuss alternative approaches for conducting targeted embedding and feature exploration to enable hypothesis-driven biological discovery.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Tue, 19 Sep 2023 16:00:00 GMT</pubDate>
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<title><![CDATA[The Biostar Herald for Wednesday, September 06, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
<div>
<a class="" href="https://www.biostars.org/u/admin-user-1/">
<img class="ui centered circular image" src="https://secure.gravatar.com/avatar/46d229b033af06a191ff2267bca9ae56?s=80&d=robohash" referrerpolicy="no-referrer">
</a>
</div>
<div class="muted">
<div>8 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
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<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Check our new paper “Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation”. <a href="https://t.co/W7GYZgGbgh">https://t.co/W7GYZgGbgh</a></p>— David Kelley (@drklly) <a href="https://twitter.com/drklly/status/1698013780394041561?ref_src=twsrc%5Etfw">September 2, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">I've been coding in Python for 8 years now. ⏳<br><br>If I were to start over again in 2023, here's a roadmap:👇 <a href="https://t.co/PszcgafCUd">pic.twitter.com/PszcgafCUd</a></p>— Akshay 🚀 (@akshay_pachaar) <a href="https://twitter.com/akshay_pachaar/status/1697225233374359646?ref_src=twsrc%5Etfw">August 31, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://galantelab.github.io/sandy/" rel="nofollow">Sandy | Sandy is a bioinformatics tool that provides a simple and extensible engine to simulate single-end and paired-end reads for whole-genome and RNA sequencing.</a> (galantelab.github.io)</h3>
<blockquote><p>Sandy is a bioinformatics tool that provides a simple engine to simulate next-generation sequencing (NGS) reads for genomic and transcriptomic pipelines. Simulated data works as experimental control - a key step to optimize NGS analysis - in comparison to hypothetical models. Sandy is a straightforward, easy-to-use, fast and highly customizable tool that generates reads requiring only a fasta file as input.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Terrifying plot for those working in microbiome profiling <a href="https://t.co/8vKXX3uacW">pic.twitter.com/8vKXX3uacW</a></p>— Mick W@tson ↙️ (@BioMickWatson) <a href="https://twitter.com/BioMickWatson/status/1696488891056820452?ref_src=twsrc%5Etfw">August 29, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41598-023-40799-x" rel="nofollow">Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data | Scientific Reports</a> (www.nature.com)</h3>
<blockquote><p>We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq.[...] These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">somalier can find relatedness among thousands (or a handful if that's what you have) of samples in seconds. latest release updates a lesser-used feature to find your own sites with which to calculate kinship: <a href="https://t.co/etNxULXsk4">https://t.co/etNxULXsk4</a><br><br>thanks <a href="https://twitter.com/johanneskoester?ref_src=twsrc%5Etfw">@johanneskoester</a> for reporting!</p>— brent pedersen (@brent_p) <a href="https://twitter.com/brent_p/status/1696075088506806608?ref_src=twsrc%5Etfw">August 28, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbad107/7252269" rel="nofollow">https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbad107/7252269</a></h3>
<blockquote><p>We introduce VCFshiny, an R package that features a user-friendly web interface enabling interactive annotation, interpretation, and visualization of variant information stored in VCF files. VCFshiny offers two annotation methods, Annovar and VariantAnnotation, to add annotations such as genes or functional impact. Annotated VCF files are deemed acceptable inputs for the purpose of summarizing and visualizing variant information.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Tue, 05 Sep 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9574254/</guid>
<link>https://www.biostars.org/p/9574254/</link>
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<title><![CDATA[The Biostar Herald for Monday, August 28, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
<div>
<a class="" href="https://www.biostars.org/u/admin-user-1/">
<img class="ui centered circular image" src="https://secure.gravatar.com/avatar/46d229b033af06a191ff2267bca9ae56?s=80&d=robohash" referrerpolicy="no-referrer">
</a>
</div>
<div class="muted">
<div>9 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad516/7251027" rel="nofollow">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad516/7251027</a></h3>
<blockquote><p>We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">A very intriguing result in the new Y chromosome paper, one that you might miss unless you read the paper closely... 1/6 <a href="https://t.co/YQt5iLIQ61">https://t.co/YQt5iLIQ61</a></p>— Steven Salzberg 💙💛 (@StevenSalzberg1) <a href="https://twitter.com/StevenSalzberg1/status/1695078983887634648?ref_src=twsrc%5Etfw">August 25, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Over 3,500 authenticated microbial genomes are currently available on the ATCC Genome Portal (<a href="https://t.co/F3UZguZ2sC">https://t.co/F3UZguZ2sC</a>) - reference genomes for 3,205 bacteria, 254 fungi, 293 viruses, and 4 protists so far. Over 100+ released every month too! :) 🧬🦠🍄🚀 <a href="https://twitter.com/hashtag/genomics?src=hash&ref_src=twsrc%5Etfw">#genomics</a> <a href="https://twitter.com/hashtag/bioinformatics?src=hash&ref_src=twsrc%5Etfw">#bioinformatics</a></p>— Jonathan Jacobs 🧬🦠🕹️🏕️ (@bioinformer) <a href="https://twitter.com/bioinformer/status/1694787161948651979?ref_src=twsrc%5Etfw">August 24, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://arxiv.org/abs/2308.07333" rel="nofollow">[2308.07333] Computational reproducibility of Jupyter notebooks from biomedical publications</a> (arxiv.org)</h3>
<blockquote><p>Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles [ ...] 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.08.21.554084v1" rel="nofollow">Flexiplex: A versatile demultiplexer and search tool for omics data | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>We developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell line specific sequences in Illumina short-read single cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools. Flexiplex is available at <a href="https://davidsongroup.github.io/flexiplex/" rel="nofollow">https://davidsongroup.github.io/flexiplex/</a>.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Sun, 27 Aug 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9573517/</guid>
<link>https://www.biostars.org/p/9573517/</link>
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<title><![CDATA[The Biostar Herald for Thursday, August 24, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
<div>
<a class="" href="https://www.biostars.org/u/admin-user-1/">
<img class="ui centered circular image" src="https://secure.gravatar.com/avatar/46d229b033af06a191ff2267bca9ae56?s=80&d=robohash" referrerpolicy="no-referrer">
</a>
</div>
<div class="muted">
<div>10 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06457-y" rel="nofollow">The complete sequence of a human Y chromosome | Nature</a> (www.nature.com)</h3>
<blockquote><p>Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Why so many names for the same contig? Isn't CM000664.2 just chr2?<br><br>Don't panic, we've got a tool for this.<br><br>fgbio CollectAlternateContigNames<a href="https://twitter.com/hashtag/Bioinformatics?src=hash&ref_src=twsrc%5Etfw">#Bioinformatics</a> <a href="https://t.co/rfjqRf7Sna">https://t.co/rfjqRf7Sna</a></p>— Nils Homer (@nilshomer) <a href="https://twitter.com/nilshomer/status/1694591605200810278?ref_src=twsrc%5Etfw">August 24, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03027-3" rel="nofollow">The CUT&RUN suspect list of problematic regions of the genome | Genome Biology | Full Text</a> (genomebiology.biomedcentral.com)</h3>
<blockquote><p>While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad480/7234613" rel="nofollow">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad480/7234613</a></h3>
<blockquote><p>In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant calling accuracy. We examine the performance of three general-purpose short-read aligners – BWA-MEM, Bowtie 2, and Arioc – in conjunction with three germline variant callers: DeepVariant, FreeBayes, and GATK HaplotypeCaller. We discuss the behavior of the read aligners with regard to the data elements on which the variant callers rely, and illustrate how the runtime configurations of these software tools combine to affect variant calling performance.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">"Data visualization is where you start and end a data analysis." -- <a href="https://twitter.com/rafalab?ref_src=twsrc%5Etfw">@rafalab</a> <a href="https://twitter.com/hashtag/JSM2023?src=hash&ref_src=twsrc%5Etfw">#JSM2023</a></p>— Stephanie Hicks (@stephaniehicks) <a href="https://twitter.com/stephaniehicks/status/1688998329256984577?ref_src=twsrc%5Etfw">August 8, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
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<pubDate>Wed, 23 Aug 2023 16:00:00 GMT</pubDate>
<guid isPermaLink="false">https://www.biostars.org/p/9573169/</guid>
<link>https://www.biostars.org/p/9573169/</link>
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<title><![CDATA[The Biostar Herald for Wednesday, August 09, 2023]]></title>
<description><![CDATA[<div class="user_box tablet right">
<div>
<a class="" href="https://www.biostars.org/u/admin-user-1/">
<img class="ui centered circular image" src="https://secure.gravatar.com/avatar/46d229b033af06a191ff2267bca9ae56?s=80&d=robohash" referrerpolicy="no-referrer">
</a>
</div>
<div class="muted">
<div>12 weeks ago</div>
<div><a href="https://www.biostars.org/u/admin-user-1/">Biostar</a>
<i class="ui muted bolt icon"></i>
2.2k
</div>
</div>
</div>
<span itemprop="text">
<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/50673/" rel="nofollow">manaswwm</a>,
and was edited by <a href="https://www.biostars.org/u/8494/" rel="nofollow">Ram</a>,
<a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
<hr>
<h3><a href="https://joss.theoj.org/papers/10.21105/joss.01762" rel="nofollow">Journal of Open Source Software: Mashtree: a rapid comparison of whole genome sequence files</a> (joss.theoj.org)</h3>
<blockquote><p>Min-hash creates distances between any two genomes, min-hash values can be used to
rapidly cluster genomes into trees using the neighbor-joining algorithm (Saitou & Nei, 1987).
We implemented this idea in software called Mashtree, which quickly and efficiently generates
large trees that would be too computationally intensive using other methods.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://github.com/vanheeringen-lab/genomepy" rel="nofollow">GitHub - vanheeringen-lab/genomepy: genes and genomes at your fingertips</a> (github.com)</h3>
<blockquote><p>genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">I think we need to talk about how devastating this cancer microbiome refutation paper from<a href="https://twitter.com/StevenSalzberg1?ref_src=twsrc%5Etfw">@StevenSalzberg1</a><br>and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/n<a href="https://t.co/wWsHTa4K8x">https://t.co/wWsHTa4K8x</a></p>— Professor Booty PhD (@ProfBootyPhD) <a href="https://twitter.com/ProfBootyPhD/status/1688386329405505536?ref_src=twsrc%5Etfw">August 7, 2023</a></blockquote>
</h3>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.biorxiv.org/content/10.1101/2023.07.26.550536v1" rel="nofollow">Challenges in identifying mRNA transcript starts and ends from long-read sequencing data | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>Here, we systematically assess the variability and accuracy of mRNA terminal ends identified by LRS reads across multiple sequencing platforms. We find substantial inconsistencies in both the start and end coordinates of LRS reads spanning a gene, such that LRS reads often fail to accurately recapitulate annotated or empirically derived terminal ends of mRNA molecules.</p>
</blockquote>
<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
<hr>
<h3><a href="https://www.nature.com/articles/s41586-023-06288-x" rel="nofollow">Evolution of a minimal cell | Nature</a> (www.nature.com)</h3>
<p>Evolution of a minimal version of a bacterial cell</p>
<p>submitted by: <a href="https://www.biostars.org/u/50673/" rel="nofollow">manaswwm</a></p>
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<pubDate>Tue, 08 Aug 2023 16:00:00 GMT</pubDate>
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<title><![CDATA[The Biostar Herald for Wednesday, August 02, 2023]]></title>
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<p>The <strong>Biostar Herald</strong> publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit <a href="https://www.biostars.org/herald/" rel="nofollow">links here</a>.</p>
<p>This edition of the Herald was brought to you by contribution from <a href="https://www.biostars.org/u/18713/" rel="nofollow">GenoMax</a>,
<a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,
<a href="https://www.biostars.org/u/134671/" rel="nofollow">Starlitnightly</a>,
and was edited by <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a>,</p>
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<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Hey Steve, What do you think of the rebuttal - <a href="https://t.co/cv44CxCnio">https://t.co/cv44CxCnio</a></p>— Jack A Gilbert (he/him/his) (@gilbertjacka) <a href="https://twitter.com/gilbertjacka/status/1686408777007030272?ref_src=twsrc%5Etfw">August 1, 2023</a></blockquote>
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<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<h3><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Major, fatal errors found in the data and methods of a 2020 paper in <a href="https://twitter.com/Nature?ref_src=twsrc%5Etfw">@Nature</a>, including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. <a href="https://twitter.com/AbrahamGihawi?ref_src=twsrc%5Etfw">@abrahamgihawi</a> <a href="https://twitter.com/elapertea?ref_src=twsrc%5Etfw">@elapertea</a> <a href="https://twitter.com/YuchenGe1?ref_src=twsrc%5Etfw">@YuchenGe1</a> <a href="https://twitter.com/JenniferLu717?ref_src=twsrc%5Etfw">@JenniferLu717</a> <a href="https://t.co/z5Aja84kiR">https://t.co/z5Aja84kiR</a></p>— Steven Salzberg 💙💛 (@StevenSalzberg1) <a href="https://twitter.com/StevenSalzberg1/status/1686350449069244416?ref_src=twsrc%5Etfw">August 1, 2023</a></blockquote>
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<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<h3><a href="https://www.biorxiv.org/content/10.1101/2023.07.28.550993v1" rel="nofollow">Major data analysis errors invalidate cancer microbiome findings | bioRxiv</a> (www.biorxiv.org)</h3>
<blockquote><p>We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cancers [...]
Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong.</p>
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<p>submitted by: <a href="https://www.biostars.org/u/2/" rel="nofollow">Istvan Albert</a></p>
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<h3><a href="https://github.com/Starlitnightly/omicverse" rel="nofollow">GitHub - Starlitnightly/omicverse: A python library for multi omics included bulk and single cell RNA-seq analysis.</a> (github.com)</h3>
<p>OmicVerse is the fundamental package for multi omics included bulk and single cell analysis with Python. The original name of the omicverse was Pyomic, but we wanted to address a whole universe of transcriptomics, so we changed the name to OmicVerse, it aimed to solve all task in RNA-seq.</p>
<p>The OmicVerse documentation website provides an application programming interface (API) reference for each algorithm, along with tutorials describing the functionality and limitations of each algorithm and its interaction with other bulk/single-seq tools. These tutorials are also accessible through Google Colab, providing a free computing environment to support pipeline studies.</p>
<p>Our aim was to create an ecosystem for bulk/single-seq analysis and beautiful visualization within Python environments. Users can perform comprehensive transcriptome analysis using a single programming language, leveraging the machine-learning models and expertise of the Python community. As OmicVerse continues to evolve, we anticipate ongoing updates that incorporate new algorithms, features, and models. OmicVerse is expected to benefit the bulk/single-seq community by facilitating the prototyping of new models, establishing standards for the analysis of trans omics, and enhancing the scientific discovery pipeline.</p>
<p>submitted by: < |
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