V-pipe

V-pipe is a tool for creating workflows to analyze next-generation sequencing (NGS) data from viral pathogens. V-pipe can output many results in various formats, such as SNV calls, local and global haplotypes, and consensus sequences. A version of the V-pipe to analyze high-throughput sequencing data of SARS-CoV-2 is available. See 'links.'

Topic

Genomics;Population genetics;Workflows

Detail

  • Operation: Sequence alignment;Genetic variation analysis

  • Software interface: Command-line user interface;Workflow

  • Language: Shell;Python

  • License: Apache-2.0

  • Cost: Free

  • Version name: 2.99.1

  • Credit: -

  • Input: Organized in a two-level directory hierarchy, and the sequencing reads must be provided in a sub-folder named raw_data.

  • Output: -

  • Contact: susana.posada@bsse.ethz.ch;david.seifert@bsse.ethz.ch;niko.beerenwinkel@bsse.ethz.ch;ivan.topolsky@sib.swiss;v-pipe@bsse.ethz.ch

  • Collection: -

  • Maturity: Stable

Publications

  • Recent advances in inferring viral diversity from high-throughput sequencing data.
  • Posada-Cespedes S, Seifert D, Beerenwinkel N. Recent advances in inferring viral diversity from high-throughput sequencing data. Virus Res. 2017 Jul 15;239:17-32. doi: 10.1016/j.virusres.2016.09.016. Epub 2016 Sep 28. PMID: 27693290.
  • https://doi.org/10.1016/j.virusres.2016.09.016
  • PMID: 27693290
  • PMC: -

Download and documentation

< Back to DB search