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-2 provides defaults to analyze SARS-CoV-2 NGS data.
  • default reference sequence is NC_045512 (identical to GeneBank entry MN908947)
  • ShoRAH 2 integrated for SNV calling
• all SNV calls are also reported as standard VCF files

Technical requirements:

• 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.

Subscribe to our newsletter to be informed about future updates.

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.