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ratblab_wgs

Bacterial assembly workflow based on ISCIII/RATB lab practices

https://github.com/daniel-vm/ratblab_wgs

Science Score: 31.0%

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Repository

Bacterial assembly workflow based on ISCIII/RATB lab practices

Basic Info
  • Host: GitHub
  • Owner: Daniel-VM
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Size: 2.24 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

WGS BACTERIAL ASSEMBLY

Bacterial assembly workflow following the RATB/ISCIII lab practices.

Documentation

See the documentation for a more detailed information of the workflow usage, paramers and output files.

Structure

The ratbLab_wgs workflow has been implemented in Nextflow DSL2.

Steps

  1. Input sample check
  2. Concatenate FastQ samples
  3. Addapter trimming Trimmomatic and quality check FastQC of short-reads
  4. Screen for contamnants with Mash

  5. Genomme assembly (de novo):

    5.1 Genome assembly of short-reads UNICYCLER

    5.2 Quality check of assemblies with QUAST

    5.3 Visualization of de novo assemblies with Bandage

  6. Workflow statistics with MultiQC

Owner

  • Name: Daniel VM
  • Login: Daniel-VM
  • Kind: user

:computer: > Bioinformatician at CIBERINFECT :chart_with_upwards_trend: > Data analyst (R)

Citation (CITATIONS.md) 

# ratbLab_wgs: 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.

## 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.

GitHub Events

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Dependencies

.github/workflows/awsfulltest.yml actions
  • nf-core/tower-action v2 composite
.github/workflows/awstest.yml actions
  • nf-core/tower-action v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
.github/workflows/linting.yml actions
  • actions/checkout v2 composite
  • actions/checkout master composite
  • actions/setup-node v2 composite
  • actions/setup-python v1 composite
  • actions/upload-artifact v2 composite
  • karancode/yamllint-github-action master composite
  • mshick/add-pr-comment v1 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/bandage/image/meta.yml cpan
modules/nf-core/cat/fastq/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gunzip/meta.yml cpan
modules/nf-core/mash/screen/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/quast/meta.yml cpan
modules/nf-core/trimmomatic/meta.yml cpan
modules/nf-core/unicycler/meta.yml cpan
subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml cpan