NASTRA

This is the code of the article Innovative Short Tandem Repeat Analysis through Cluster-Based Structure-Aware Algorithm in Nanopore Sequencing Data.

In this repository, we provide a STR genotyping method for forensic-level accuracy.

Table of content

• NASTRA
  • Table of Contents
  • Installation and Test
  • Usage
  • Citation

Installation and Test

In this part, we introcduce the installation step and test the code for NASTRA. We use conda to manage the computing environment, and install samtools v1.9 firstly via the bioconda channel.

Once finish the installtion step, we provide the alignment files of eight standard cell lines for code test (barcode01-08). Additionally, the files are downsampled using NanoTime, which is described in the article.

# download the source code, the size of test data is ~67Mb, this may be time-consuming
git clone https://github.com/renzilin/NASTRA.git

# enter the directory
cd NASTRA

# install dependencies. Only test on Ubuntu System (samtools can't be install via conda for ARM)
conda env create -n nastra_env -f env.yaml

# code test
conda activate nastra_env

# sample-level parallelization using xargs
seq -w 01 08 | xargs -P 8 -L 1 -I {} python NASTRA/nastra.py call -b test_data/alignment_8standards_1h/barcode{}.bam -o test_data/nastra_out/barcode{}.txt;

The sample information of BAM files is listed below:

File name	Sample
barcode01.bam	NA12878
barcode02.bam	NA24143
barcode03.bam	NA24149
barcode04.bam	NA24694
barcode05.bam	NA24695
barcode06.bam	9947A
barcode07.bam	9948
barcode08.bam	2800M

Usage

The nastra.py requires several options:

1. required: the path of BAM file, usually generated by minimap2.
2. required: the path of output file.
3. optional: the path of factsheet, storing the information of repeat motifs of STRs. We provide a revised file NASTRA/cfgs/repeat_structure.pat. Assessible in NIST STRBase FactSheet.
4. optional: the path of panel file, storing the positional information of STRs. We provide a revised file NASTRA/cfgs/panel_forenseq.csv.
5. optional: the path of config file of SN, storing the optimal thresholds for NASTRA. We provide one in NASTRA/cfgs/threshold.cfg, which was utilized in our manusctipts.
6. optional: the predefined SN threshold used for quality control, default is 25.
7. optional: the path of samtools, which is required to extract aligned reads.

usage: nastra.py call [-h] -b BAM [-f FACTSHEET] [-p PANEL] [-c CONFIG] -o OUTPUT [--samtools SAMTOOLS] [--sncutoff SNCUTOFF]

optional arguments:
  -h, --help            show this help message and exit
  -b BAM, --bam BAM     the path of bam file
  -f FACTSHEET, --factsheet FACTSHEET
                        the path of STR factsheet
  -p PANEL, --panel PANEL
                        the path of the loci panel file
  -c CONFIG, --config CONFIG
                        the config file of SN cutoff
  -o OUTPUT, --output OUTPUT
                        the path of output
  --samtools SAMTOOLS   the PATH to samtools

Citiing NASTRA

Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang, Pingping Sun, Jiguo Xue, Xiaochen Bo, Bo Zhou, Jiangwei Yan, Ming Ni, NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm, Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae472, https://doi.org/10.1093/bib/bbae472