We have released a new version of V-pipe specifically adapted to analyze high-throughput sequencing data of SARS-CoV-2.
- available in the sars-cov2 branch of the Github repository
- default reference sequence is NC_045512, identical to GenBank entry MN908947
- default configuration file assumes SARS-CoV-2 NGS data
- new version ShoRAH 2 integrated for SNV calling
- 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 (see tutorial). 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).
The V-pipe sars-cov2 branch 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.