# 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

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:link: documentation/installation
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Installation 
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Install V-pipe with conda or docker and get started with the basics.
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:link: tutorials/tutorial_hiv
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HIV tutorial
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Tutorial on analyzing HIV data with V-pipe.

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:link: tutorials/tutorial_sarscov2
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SARS-CoV-2 tutorial
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Tutorial on analyzing SARS-CoV-2 data with V-pipe.
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:link: tutorials/tutorial_cowwid
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SARS-CoV-2 waste water tutorial
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Tutorial on analyzing SARS-CoV-2 waste water data with V-pipe.

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## 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](https://github.com/cbg-ethz/V-pipe/issues) on GitHub 
- Ask a question on [Gitter](https://gitter.im/V-pipe/community)
- Subscribe to the [mailing list](https://sympa.ethz.ch/sympa/info/v-pipe-users)
- Directly contact the developers: [v-pipe@bsse.ethz.ch](mailto:v-pipe@bsse.ethz.ch)

## Citing V-pipe

For citing the latest version of V-pipe refer to {cite}`fuhrmann_v-pipe_2023` or the first paper describing the pipeline {cite}`posada-cespedes_v-pipe_2021`.