V-pipe#
V-pipe is a bioinformatics pipeline that integrates various computational tools for the analysis of viral high-throughput sequencing data. It supports the reproducible analysis of genomic diversity in intra-host virus populations, which is often involved in viral pathogenesis and virulence. V-Pipe takes as an input raw data in FASTQ format and depending on the user-defined configuration will output consensus sequences, SNV calls and local/global haplotypes.
Getting started#
Installation
Install V-pipe with conda or docker and get started with the basics.
HIV tutorial
Tutorial on analyzing HIV data with V-pipe.
SARS-CoV-2 tutorial
Tutorial on analyzing SARS-CoV-2 data with V-pipe.
SARS-CoV-2 waste water tutorial
Tutorial on analyzing SARS-CoV-2 waste water data with V-pipe.
Support#
Are you running into issues? Or want to stay up-to-date with the latest developments? Here are some ways to get in touch:
Write an issue on GitHub
Ask a question on Gitter
Subscribe to the mailing list
Directly contact the developers: v-pipe@bsse.ethz.ch
Citing V-pipe#
For citing the latest version of V-pipe refer to [Fuhrmann et al., 2023] or the first paper describing the pipeline [Posada-Céspedes et al., 2021].