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genomeskim

https://github.com/nhm-london-bioinformatics/genomeskim

Science Score: 54.0%

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    Found 10 DOI reference(s) in README
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    Links to: ncbi.nlm.nih.gov
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Repository

Basic Info
  • Host: GitHub
  • Owner: NHM-London-Bioinformatics
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Size: 15.1 MB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/genomeskim

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

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Introduction

nf-core/genomeskim is a bioinformatics pipeline that is designed for batch processing of low-coverage genomic DNA sequencing. It is currently designed for and tested on Illumina sequencing data, and takes as input raw sequence reads from shotgun sequencing of a single individual in order to 1. assemble, validate and annotate putative organelle genomes and 2. calculate summary genome statistics based on the non-organellar reads recovered.

nf-core/genomeskim workflow overview

By default, the pipeline currently performs the following:

  1. Read QC (FastQC)
  2. Adapter trimming (FastP)
  3. Organelle assembly (GetOrganelle)
  4. Taxonomic and coverage validation of contigs (BLAST, Minimap2, Blobtoolkit)
  5. Annotation of mitogenomes only (MITOS2)
  6. Nuclear genome summary statistics (Jellyfish, Genomescope2)
  7. Pipeline QC summaries (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,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

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

Second, you need to know what sort of organellar genome you're trying to assemble, its genetic code and select a database to use for annotation.

Now, you can run the pipeline using:

```bash nextflow run nf-core/genomeskim \ -profile \ --input samplesheet.csv \ --outdir \ --getorganellegenometype \ --mitosgeneticcode \ --mitosrefdbid \ --skipvalidation

```

This minimal example skips validation as this requires further input files. If you want to undertake taxonomic validation, you need a BLAST database to compare against and a local copy of NCBI taxdump.

[!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.

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

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/genomeskim was originally written by Thomas J. Creedy, based in part on a pipeline developed by Oliver White, for use at the Natural History Museum.

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

Silvia Salatino, Matt Clark, Raju Misra

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #genomeskim channel (you can join with this invite).

Citations

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

You can cite the nf-core publication as follows:

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: NHM London - Bioinformatics
  • Login: NHM-London-Bioinformatics
  • Kind: organization
  • Email: s.salatino@nhm.ac.uk

Citation (CITATIONS.md) 

# nf-core/genomeskim: 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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