zongzhiwu/what_the_phage

WtP: Phage identification via nextflow and docker or singularity

What the Phage (WtP)

• by Christian Brandt & Mike Marquet
• this tool is under active development,feel free to report issues and add suggestions
• Use a release candidate for a stable experience via -r e.g. -r v1.0.0
  • These are extensively tested release versions of WtP
  • releases of WtP are listed here

Preprint:

What the Phage: A scalable workflow for the identification and analysis of phage sequences

M. Marquet, M. Hölzer, M. W. Pletz, A. Viehweger, O. Makarewicz, R. Ehricht, C. Brandt

doi: https://doi.org/10.1101/2020.07.24.219899

What is this repo

TL;DR

• WtP is a scalable and easy-to-use workflow for phage identification and analysis. Our tool currently combines 10 established phage identification tools
• An attempt to streamline the usage of various phage identification and prediction tools
• The main focus is stability and data filtering/analysis for the user
• The tool is intended for fasta and fastq reads to identify phages in contigs/reads
• Proper prophage detection is not implemented (yet) - but a handful of tools report them - so they are mostly identified

A detailed documentation can be found here

• The documentation contains:
  • General information
  • Installation guide
  • Tool overview
  • Result interpretation
  • Troubleshooting