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wes-relation

https://github.com/philge/wes-relation

Science Score: 18.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
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    Scientific vocabulary similarity
    Low similarity (4.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: philge
  • License: mit
  • Language: HTML
  • Default Branch: main
  • Size: 3.16 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

Nextflow code for comparing WES samples. Steps to run the pipeline are described below.

Prerequisites to run Nextflow code

Install Anaconda
Create a conda environment
Install Nextflow in conda environment
Clone https://github.com/philge/wes-relation.git
Change directory to Nextflow code folder (./wes-relation), prepare samplesheet.csv

Run command:
console nextflow run main.nf --input samplesheet.csv -with-report run_report.html --outdir results --fasta /*/genome.fa -resume -profile conda

Credits

Code was originally written by Philge Philip.

Contributions and Support

AUTHORS:

Philge Philip philgev2@gmail.com

Owner

  • Name: Philge Philip
  • Login: philge
  • Kind: user
  • Location: Chennai, India
  • Company: @Excelra

Senior Scientific Manager, Excelra

Citation (CITATIONS.md) 

# nf-core/wes-relation: 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/)

- [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.

- [bam2FastQ](https://genome.sph.umich.edu/wiki/BamUtil:_bam2FastQ))
- [cat]
- [Canu] (https://github.com/marbl/canu)
- [Purge_dups] (https://github.com/dfguan/purge_dups)
- [busco] (https://busco.ezlab.org/)
- [merqury] (https://github.com/marbl/merqury)
- [assembly-stats] (https://github.com/rjchallis/assembly-stats)

## 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)

- [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.

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Dependencies

modules/nf-core/modules/fastqc/meta.yml cpan