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annotationpipeline

Annotation of bacterial genomes using Bakta, EggNOG mapper, Cayman and VFDB

https://github.com/barbarahelena/annotationpipeline

Science Score: 44.0%

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Repository

Annotation of bacterial genomes using Bakta, EggNOG mapper, Cayman and VFDB

Basic Info
  • Host: GitHub
  • Owner: barbarahelena
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 369 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 9 months ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

annopipeline

Nextflow run with conda run with docker run with singularity

Introduction

annopipeline is a bioinformatics pipeline that performs functional annotation of genomes and bacterial metagenomes. It annotates proteins using Bakta, and the Bakta output is then used for further functional annotation of the proteins using eggNOG-mapper, Cayman, and VFDB. The pipeline is designed to be flexible and can be run on a variety of platforms, including local machines and clusters.

  1. Annotation of genomes using Bakta (Bakta)
  2. EggNOG functional annotation of the proteins (eggNOG-mapper)
  3. Cayman carbohydrate active enzymes (CAZy) profiling of proteins (Cayman)
  4. Virulence factor annotation profiling using VFDB (VFDB) and Diamond (Diamond) <!-- 5. Present QC for raw reads and Diamond (MultiQC) -->

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.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fasta Sample1,/path/to/sample1.fasta

Each row represents either an assembly fasta or Bakta .faa output (to skip the Bakta step).

Now, for assemblies, you can run the pipeline using:

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

If you already have Bakta output files, you can provide the Bakta .faa files in the samplesheet and skip the Bakta step by using the --annotation false parameter:

bash nextflow run annopipeline \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR> \ --annotation false

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

Credits

annopipeline was originally written by Barbara Verhaar and Kyanna Ouyang. If you would like to contribute to this pipeline, please open a pull request or issue.

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

Owner

  • Name: Barbara Verhaar
  • Login: barbarahelena
  • Kind: user
  • Location: Amsterdam

PhD candidate @ Amsterdam UMC Vascular medicine

Citation (CITATIONS.md) 

# annopipeline: 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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Dependencies

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modules/local/bakta/bakta/meta.yml cpan
modules/local/bakta/baktadbdownload/meta.yml cpan
modules/nf-core/diamond/blastp/meta.yml cpan
modules/nf-core/diamond/makedb/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/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_nfschema_plugin/meta.yml cpan
modules/local/bakta/bakta/environment.yml pypi
modules/local/bakta/baktadbdownload/environment.yml pypi
modules/nf-core/diamond/blastp/environment.yml pypi
modules/nf-core/diamond/makedb/environment.yml pypi
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi