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genealignment

An NF-core pipeline to alignment genesets against a given reference genome.

https://github.com/sanger-tol/genealignment

Science Score: 65.0%

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    Found 10 DOI reference(s) in README
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    Organization sanger-tol has institutional domain (www.sanger.ac.uk)
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    Low similarity (12.8%) to scientific vocabulary

Keywords

gene-alignment genomics nextflow pipeline
Last synced: 7 months ago · JSON representation ·

Repository

An NF-core pipeline to alignment genesets against a given reference genome.

Basic Info
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gene-alignment genomics nextflow pipeline
Created almost 2 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Introduction

sanger-tol/genealignment is a bioinformatics pipeline that generated geneset alignments to a specified input genome. This pipeline will be used for evaluating genesets for use in TreeVal

  1. YAML_INPUT -- Parses the input yaml into Channels for downstream use.
  2. GENERATE_GENOME -- Generates a trimmed fasta index file for us in JBrowse.
  3. GENE_ALIGNMENT -- Align geneset data against the input genome.

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.

Much of the information regarding running this pipeline can be found on the TreeVal usage page.

The input yaml should consist of the following:

assembly: assem_level: scaffold assem_version: 1 sample_id: Oscheius_DF5033 latin_name: to_provide_taxonomic_rank defined_class: nematode project_id: DTOL reference_file: TOLID.fasta alignment: data_dir: /path/to/gene_alignment_data/ common_name: "" # For future implementation (adding bee, wasp, ant etc) geneset_id: "OscheiusTipulae.ASM1342590v1,CaenorhabditisElegans.WBcel235,Gae_host.Gae" intron: size: "50k"

Now, you can run the pipeline using:

bash nextflow run sanger-tol/genealignment \ -profile <docker/singularity/.../institute> \ --input samplesheet.yaml \ --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

sanger-tol/genealignment was originally written by DLBPointon.

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: Tree of Life programme
  • Login: sanger-tol
  • Kind: organization
  • Location: United Kingdom

The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology

Citation (CITATIONS.md) 

# sanger-tol/genealignment: 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.

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