Since version v2.99.0, V-pipe integrates specific adaptations to analyze high-throughput sequencing data of SARS-CoV-2:
- available in the master branch of the Github repository and in the releases
- the virus base configuration
sars-cov-2provides defaults to analyze SARS-CoV-2 NGS data.
- all SNV calls are also reported as standard VCF files
- Hardware: recommended RAM >= 16GiB, Storage >= 40 GiB (actual space usage depends on datasets size).
- OS: Linux and Mac OS X currently supported (Windows 10 users can install Windows Subsystem for Linux as bioconda does not support Windows directly).
- Software: miniconda and snakemake required; we strongly encourage our users to deploy the pipeline using the quick install script. All dependencies are automatically downloaded and installed by snakemake from bioconda.
The tutorial demonstrates how to use V-pipe (specifically for SARS-CoV-2 data).
V-pipe is continuously updated with improvements and extensions, including on the visualization and reporting of results.
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V-pipe is part of the SIB resources supporting SARS-CoV-2 research, used to process NGS data for the Swiss SARS-CoV-2 Sequencing Consortium (S3C) and for the Surveillance of SARS-CoV-2 genomic variants in wastewater.