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gunc_workflow

GUNC pipeline

https://github.com/grp-bork/gunc_workflow

Science Score: 75.0%

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

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    CITATION.cff file
    Found CITATION.cff file
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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
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    Institutional organization owner
    Organization grp-bork has institutional domain (www.bork.embl.de)
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

GUNC pipeline

Basic Info
  • Host: GitHub
  • Owner: grp-bork
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 27.4 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

GUNC workflow

Bork Group Logo Developed by the Bork Group in collaboration with nf-core
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The development of this workflow was supported by NFDI4Microbiota NFDI4Microbiota icon

Description

The GUNC workflow is a nextflow workflow for the detection of chimerism & contamination in prokaryotic genomes resulting from mis-binning of contigs from unrelated lineages. The workflow is based on the CheckM and GUNC (Genome UNClutterer) tools. GUNC applies an entropy based score on taxonomic assignment and the contig location of all genes in a genome.

Citation

This workflow: DOI

Also cite: Orakov A, Fullam A, Coelho LP, et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 2021;22(1):178. Published 2021 Jun 13. doi:10.1186/s13059-021-02393-0 Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043-1055. doi:10.1101/gr.186072.114 Ewels PA, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276-278. doi:10.1038/s41587-020-0439-x

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

Overview

  1. Run CheckM (CheckM)
  2. Run GUNC (GUNC)

Usage

Cloud-based Workflow Manager (CloWM)

This workflow will be available on the CloWM platform (coming soon).

Command-Line Interface (CLI)

You can run the pipeline using: bash nextflow run gunc \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

Input files

The input is a csv samplesheet with your input data that looks as follows:

samplesheet.csv:

csv id,group,assembler,fasta test_minigut,0,MEGAHIT,https://github.com/nf-core/test-datasets/raw/mag/assemblies/MEGAHIT-test_minigut.contigs.fa.gz

Each row represents a metagenomic bin.

Owner

  • Name: Bork Group at EMBL Heidelberg
  • Login: grp-bork
  • Kind: organization
  • Location: Germany

Citation (CITATIONS.md) 

# nf-core/gunc: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Push event: 297
Last Year
  • Push event: 297

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
.github/workflows/release-announcments.yml actions
  • actions/setup-python v4 composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action v0.0.2 composite
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
pyproject.toml pypi
.github/workflows/github-repo-stats.yml actions
  • jgehrcke/github-repo-stats RELEASE composite
modules/nf-core/aria2/meta.yml cpan
modules/nf-core/checkm/lineagewf/meta.yml cpan
modules/nf-core/checkm/qa/meta.yml cpan
modules/nf-core/gunc/downloaddb/meta.yml cpan
modules/nf-core/gunc/mergecheckm/meta.yml cpan
modules/nf-core/gunc/run/meta.yml cpan
modules/nf-core/aria2/environment.yml conda
  • aria2 1.36.0.*
modules/nf-core/checkm/lineagewf/environment.yml conda
  • checkm-genome 1.2.2.*
modules/nf-core/checkm/qa/environment.yml conda
  • checkm-genome 1.2.2.*
modules/nf-core/gunc/downloaddb/environment.yml conda
  • gunc 1.0.5.*
modules/nf-core/gunc/mergecheckm/environment.yml conda
  • gunc 1.0.5.*
modules/nf-core/gunc/run/environment.yml conda
  • gunc 1.0.5.*