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metagear-pipeline

MetaGEAR: Metagenomic Exploration and Research

https://github.com/schirmer-lab/metagear-pipeline

Science Score: 57.0%

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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 7 DOI reference(s) in README
  • ○
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  • ○
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    Low similarity (13.6%) to scientific vocabulary

Keywords

metagear metagenomics pipeline
Last synced: 6 months ago · JSON representation ·

Repository

MetaGEAR: Metagenomic Exploration and Research

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metagear metagenomics pipeline
Created over 1 year ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

schirmer-lab/metagear

GitHub Actions CI Status GitHub Actions Linting Status nf-test

Nextflow run with docker run with singularity

Introduction

schirmer-lab/metagear is a bioinformatics pipeline for comprehensive metagenomic analysis. The pipeline processes shotgun metagenomic sequencing data through quality control, taxonomic profiling, functional annotation, and gene-centric analysis workflows.

[!TIP] For easy installation, configuration, and usage, please refer to the streamlined documentation and wrapper at: schirmer-lab/metagear

The pipeline includes the following main workflows:

  1. Database Download - Install required databases (Kneaddata, MetaPhlAn, HUMAnN)
  2. Quality Control - DNA/RNA quality assessment and trimming
  3. Microbial Profiles - Taxonomic and functional profiling using MetaPhlAn and HUMAnN
  4. Gene Analysis - Gene-centric analysis workflow with optional contig catalogs

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

[!IMPORTANT] > For simplified usage and configuration, please use the wrapper and documentation at: schirmer-lab/metagear

Quick Start

Prepare a samplesheet with your input data:

samplesheet.csv:

csv sample,fastq_1,fastq_2 SAMPLE1,sample1_R1.fastq.gz,sample1_R2.fastq.gz SAMPLE2,sample2_R1.fastq.gz,sample2_R2.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

bash nextflow run schirmer-lab/metagear \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

schirmer-lab/metagear was originally written by Shen Jin, Emilio Rios, Svenja Schorlemmer.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

  • Name: Schirmer Lab
  • Login: schirmer-lab
  • Kind: organization
  • Location: Germany

Computational Microbiome Research

Citation (CITATIONS.md) 

# schirmer-lab/metagear: 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

- [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

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Last Year
  • Create event: 6
  • Issues event: 1
  • Release event: 2
  • Watch event: 1
  • Delete event: 5
  • Issue comment event: 17
  • Public event: 1
  • Push event: 13
  • Pull request review event: 3
  • Pull request event: 14
  • Fork event: 1

Dependencies

modules/nf-core/multiqc/environment.yml conda
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modules/local/cdhit/cdhit/meta.yml cpan
modules/local/cdhit/cdhitest/meta.yml cpan
modules/local/gtdbtk/classifywf/meta.yml cpan
modules/local/interproscan/meta.yml cpan
modules/local/megahit/meta.yml cpan
modules/local/metaphlan4.1/makedb/meta.yml cpan
modules/local/metaphlan4.1/metaphlan/meta.yml cpan
modules/nf-core/bwa/index/meta.yml cpan
modules/nf-core/bwamem2/index/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/prodigal/meta.yml cpan
modules/nf-core/seqkit/split2/meta.yml cpan
modules/nf-core/trimgalore/meta.yml cpan
modules/local/cdhit/cdhit/environment.yml pypi
modules/local/cdhit/cdhitest/environment.yml pypi
modules/local/gtdbtk/classifywf/environment.yml pypi
modules/local/interproscan/environment.yml pypi
modules/local/megahit/environment.yml pypi
modules/local/metaphlan4.1/makedb/environment.yml pypi
modules/local/metaphlan4.1/metaphlan/environment.yml pypi
modules/nf-core/bwa/index/environment.yml pypi
modules/nf-core/bwamem2/index/environment.yml pypi
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/prodigal/environment.yml pypi
modules/nf-core/seqkit/split2/environment.yml pypi
modules/nf-core/trimgalore/environment.yml pypi
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