Since version v2.99.0, V-pipe integrates specific adaptations to analyze high-throughput sequencing data of SARS-CoV-2:

Technical requirements:

The tutorial demonstrates how to use V-pipe (specifically for SARS-CoV-2 data).

Note: tutorial has been written written for the older sars-cov2 branch, see V-pipe’s documentation to adapt to the current newer versions of V-pipe.

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.