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ena2eggnog

eggNOG mapper pipeline

https://github.com/grp-bork/ena2eggnog

Science Score: 75.0%

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    Found 7 DOI reference(s) in README
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    Links to: zenodo.org
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    Organization grp-bork has institutional domain (www.bork.embl.de)
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    Low similarity (6.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

eggNOG mapper pipeline

Basic Info
  • Host: GitHub
  • Owner: grp-bork
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 29.4 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created about 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

ENA2eggNOG workflow

Bork Group Logo Developed by the Bork Group in collaboration with nf-core
Raise an issue or contact us

See our other Software & Services 		Contributors:
 Collaborators:
The development of this workflow was supported by NFDI4Microbiota NFDI4Microbiota icon

Description

The ENA2eggNOG workflow is a nextflow workflow for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only.

Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes, or even metagenomic gene catalogs.

The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).

Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan can be found here.

Citation

This workflow: DOI

Also cite: Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021;38(12):5825-5829. doi:10.1093/molbev/msab293 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 Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31(10):1674-1676. doi:10.1093/bioinformatics/btv033 Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. Published 2010 Mar 8. doi:10.1186/1471-2105-11-119 An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

Overview

  1. Download data from ENA/SRA (fetchngs)
  2. Run assembly (MEGAHIT)
  3. Predict genes(Prodigal)
  4. Annotate genes (eggnog-mapper)

Usage

Cloud-based Workflow Manager (CloWM)

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

Command-Line Interface (CLI)

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.

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

Input files

The input is a csv file with a list of ENA accession IDs that looks as follows:

ids.csv:

csv PRJEB6102 SRR9984183 SRR13191702

Each can be a project ID or a run ID.

Owner

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

Citation (CITATIONS.md) 

# nf-core/eggnogmapper: 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

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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/local/eggnogmapper/downloaddb/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/custom/sratoolsncbisettings/meta.yml cpan
modules/nf-core/eggnogmapper/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/megahit/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/prodigal/meta.yml cpan
modules/nf-core/sratools/fasterqdump/meta.yml cpan
modules/nf-core/sratools/prefetch/meta.yml cpan
subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan
pyproject.toml pypi
.github/workflows/github-repo-stats.yml actions
  • jgehrcke/github-repo-stats RELEASE composite
modules/local/eggnogmapper/downloaddb/environment.yml pypi
modules/nf-core/custom/sratoolsncbisettings/environment.yml pypi
modules/nf-core/eggnogmapper/environment.yml pypi
modules/nf-core/megahit/environment.yml pypi
modules/nf-core/prodigal/environment.yml pypi
modules/nf-core/sratools/fasterqdump/environment.yml pypi
modules/nf-core/sratools/prefetch/environment.yml pypi