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https://github.com/replikation/What_the_Phage

WtP: Phage identification via nextflow and docker or singularity
https://github.com/replikation/What_the_Phage

bioinformatics nextflow nextflow-pipelines phage-identification phage-sequences phages

Last synced: about 1 month ago
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WtP: Phage identification via nextflow and docker or singularity

Host: GitHub
URL: https://github.com/replikation/What_the_Phage
Owner: replikation
License: gpl-3.0
Created: 2019-08-04T18:31:54.000Z (almost 5 years ago)
Default Branch: master
Last Pushed: 2024-02-20T09:15:11.000Z (4 months ago)
Last Synced: 2024-02-20T10:32:51.825Z (4 months ago)
Topics: bioinformatics, nextflow, nextflow-pipelines, phage-identification, phage-sequences, phages
Language: Nextflow
Homepage: https://mult1fractal.github.io/wtp-documentation/
Size: 39.1 MB
Stars: 97
Watchers: 7
Forks: 16
Open Issues: 19
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff

Lists

awesome-phages - WTP - What the Phage is a scalable workflow that combines multiple prophage prediction programs, including several of the aforementioned. It starts out of the raw fasta or fastq files and generates an integrated summary of the results obtained from each of the selected tools. (Annotation / Prophage prediction)

README

        ![logo](figures/logo-wtp_small.png)

![](https://img.shields.io/github/v/release/replikation/What_the_Phage)

![](https://img.shields.io/badge/licence-GPL--3.0-lightgrey.svg)

![](https://github.com/replikation/What_the_Phage/workflows/Syntax_check/badge.svg)

![](https://img.shields.io/badge/nextflow-20.07.1-brightgreen)

![](https://img.shields.io/badge/uses-docker-blue.svg)

![](https://img.shields.io/badge/uses-singularity-yellow.svg)

[![Generic badge](https://img.shields.io/badge/Publication-Gigascience-blueviolet.svg)](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac110/6833029)

[![Generic badge](https://img.shields.io/badge/Documentation-available-purple.svg)](https://mult1fractal.github.io/wtp-documentation/)

[![Twitter Follow](https://img.shields.io/twitter/follow/gcloudChris.svg?style=social)](https://twitter.com/gcloudChris) 

[![Twitter Follow](https://img.shields.io/twitter/follow/mult1fractal.svg?style=social)](https://twitter.com/mult1fractal) 

# 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 v1.2.0`

  * These are extensively tested release versions of WtP

  * [releases of WtP are listed here](https://github.com/replikation/What_the_Phage/releases)  

## Publication:

> **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/10.1093/gigascience/giac110

# What is this repo

#### TL;DR

* WtP is a scalable and easy-to-use workflow for phage identification and analysis. Our tool currently combines 12 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 assembled fasta files to predict phages in contigs

* Proper prophage detection is not implemented - but CheckV reports them

* A full report can be found [here](https://replikation.github.io/What_the_Phage/)



    

        



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# Documentation 

* The [documentation](https://mult1fractal.github.io/wtp-documentation/) contains:

  * General information 

  * Installation guide

  * Tool overview

  * Result interpretation

  * Troubleshooting