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what_the_phage

WtP: Phage identification via nextflow and docker or singularity

https://github.com/replikation/what_the_phage

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
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  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

bioinformatics nextflow nextflow-pipelines phage-identification phage-sequences phages
Last synced: 6 months ago · JSON representation ·

Repository

WtP: Phage identification via nextflow and docker or singularity

Basic Info
Statistics
  • Stars: 106
  • Watchers: 6
  • Forks: 15
  • Open Issues: 19
  • Releases: 22
Topics
bioinformatics nextflow nextflow-pipelines phage-identification phage-sequences phages
Created over 6 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

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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

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

Documentation

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

Owner

  • Name: Christian Brandt
  • Login: replikation
  • Kind: user
  • Location: Germany
  • Company: @nanozoo and IIMK@UHJ

postDoc @ IIMK UHJ

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Marquet"
  given-names: "Mike"
- family-names: "Hölzer"
  given-names: "Martin"
- family-names: "Pletz"
  given-names: "Mathias W."
- family-names: "Viehweger"
  given-names: "Adrian"
- family-names: "Makarewicz"
  given-names: "Oliwia"
- family-names: "Ehricht"
  given-names: "Ralf"
- family-names: "Brandt"
  given-names: "Christian"
title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences"
version: v1.2.0
date-released: 2022-11-18
url: "https://github.com/replikation/What_the_Phage"
preferred-citation:
  type: article
  authors:
  - family-names: "Marquet"
    given-names: "Mike"
  - family-names: "Hölzer"
    given-names: "Martin"
  - family-names: "Pletz"
    given-names: "Mathias W."
  - family-names: "Viehweger"
    given-names: "Adrian"
  - family-names: "Makarewicz"
    given-names: "Oliwia"
  - family-names: "Ehricht"
    given-names: "Ralf"
  - family-names: "Brandt"
    given-names: "Christian"
  doi: "10.1093/gigascience/giac110"
  journal: "Gigascience"
  month: 11
  title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences"
  year: 2022
  issn: 2047-217X

GitHub Events

Total
  • Create event: 3
  • Issues event: 1
  • Release event: 1
  • Watch event: 3
  • Issue comment event: 9
  • Push event: 13
  • Pull request event: 2
Last Year
  • Create event: 3
  • Issues event: 1
  • Release event: 1
  • Watch event: 3
  • Issue comment event: 9
  • Push event: 13
  • Pull request event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mult1fractal (2)
  • hoelzer (2)
  • replikation (1)
  • gabriellovate (1)
  • boegel (1)
  • 444thLiao (1)
  • marineLZ (1)
  • xykb86 (1)
  • deminatanja (1)
  • sxh1136 (1)
Pull Request Authors
  • mult1fractal (2)
  • hoelzer (1)
Top Labels
Issue Labels
enhancement (5) documentation (4) bug (1)
Pull Request Labels

Dependencies

.github/workflows/nextflow-test.yml actions
  • actions/checkout v1 composite
phage-tool-Dockerfiles/DeepVirFinder/Dockerfile docker
  • continuumio/miniconda3 latest build
phage-tool-Dockerfiles/MARVEL/Dockerfile docker
  • continuumio/miniconda3 latest build
phage-tool-Dockerfiles/MetaPhinder/Dockerfile docker
  • ubuntu bionic build
phage-tool-Dockerfiles/PPR-Meta/Dockerfile docker
  • ubuntu bionic build
phage-tool-Dockerfiles/R-docker/Dockerfile docker
  • rocker/verse latest build
phage-tool-Dockerfiles/Virfinder/Dockerfile docker
  • rocker/verse latest build
phage-tool-Dockerfiles/seeker/Dockerfile docker
  • continuumio/miniconda3 latest build
phage-tool-Dockerfiles/virsorter/Dockerfile docker
  • continuumio/miniconda3 latest build
phage-tool-Dockerfiles/virsorter2/Dockerfile docker
  • continuumio/miniconda3 latest build