nextstrain.org/rsv

This is the Nextstrain build for respiratory syncytial virus (RSV). Output from this build is available at nextstrain.org/rsv.

Input Data

Input metadata and sequences for RSV-A and RSV-B are available via https://data.nextstrain.org

• RSV-A sequences

• RSV-A metadata

• RSV-B sequences

• RSV-B metadata

These data are generously shared by labs around the world and deposited in NCBI genbank by the authors. Please contact these labs first if you plan to publish using these data. RSV sequences and metadata can be downloaded in the /ingest folder using nextstrain build --cpus 1 ingest or nextstrain build --cpus 1 . if running directly from the /ingest directory.

The ingest pipeline is based on the Nextstrain mpox ingest workflow (https://github.com/nextstrain/mpox/tree/master/ingest). Running the ingest pipeline produces ingest/data/{a,b}/metadata.tsv and ingest/data/{a,b}/sequences.fasta.

ingest/vendored

This repository uses git subrepo to manage copies of ingest scripts in ingest/vendored, from nextstrain/ingest. To pull new changes from the central ingest repository, first install git subrepo, then run:

See ingest/vendored/README.md for instructions on how to update the vendored scripts.

Run Analysis Pipeline

The workflow produces whole genome and G gene trees for RSV-A and RSV-B. To run the workflow, use snakemake -j4 -p --configfile config/configfile.yaml and nextstrain view auspice to visualise results.

Installation

Follow the standard installation instructions for Nextstrain's suite of software tools.

Data use

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances.

Update example data

Example data is used by CI. It can also be used as a small subset of real-world data.

Example data should be updated every time metadata schema is changed. To update, run:

nextstrain build --docker . update_example_data -F

Sending data to the nextclade_data repo

From within the destination directory, run

rsync -a <path-to>/rsv/nextclade/datasets/ .

Updates for lab samples analysis:

To construct a tree with an addition of lab samples, the annotation and the sequences have to be located in input_lab_samples/{a_or_b}/ with the following names:

• comb_ann.tsv,
• nextclade_results.tsv,
• sequences.fasta

comb_ann contains NGS_ID column, which is later used as an index. nextclade_results.tsv is a standard nextclade output.

The pipeline then concatenates these sequences and annotation with the opensource ones, constructs a tree for all lab samples + a selected number of background open-source ones. Otherwise, the pipeline works as the master one.