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hicplas

https://github.com/mayee123/hicplas

Science Score: 44.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: mayee123
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 7.59 MB
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Created about 1 year ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Code of conduct Citation

docs/README.md

HiCPlas: Documentation

Nextflow pipeline for reconstructing plasmids and associating them to their bacterial host using Hi-C metagenomic data

Usage

Input

This pipeline takes as input a samplesheet containing paths to the metagenomic reads. This samplesheet is the same as one would include for nf-core/MAG and include these columns: "sample,group,shortreads1,shortreads2,longreads". Paths to shortreads2 and longreads are optional. Additionally, a path to the paired Hi-C reads must be specified under the --hic_read flag.

Parameters

--outdir: output folder -enzyme (optional): Case-sensitive enzyme name. Use multiple times for multiple enzymes --hybrid(true or false):Assemble using hybrid reads. Default false

Example Usage

sh nextflow run main.nf -profile singularity -c custom.config --input path_to_samplesheet.csv --outdir HiCPlas_results --hic_read "path_to_hic_read/sample_{1,2}.fastq.gz

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  • Login: mayee123
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Citation (CITATIONS.md) 

# nf-core/hicplas: 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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Dependencies

modules/local/kraken2/kraken2/meta.yml cpan
modules/nf-core/bwa/index/meta.yml cpan
modules/nf-core/bwa/mem/meta.yml cpan
modules/nf-core/checkm/lineagewf/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/samtools/view/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_nfvalidation_plugin/meta.yml cpan
modules/local/bbmap/bbduk/meta.yml cpan
modules/local/mobsuite/recon/meta.yml cpan
modules/local/bbmap/bbduk/environment.yml conda
  • bbmap 39.18.*
  • pigz 2.8.*
modules/local/mobsuite/recon/environment.yml conda
  • mob_suite 3.0.3.*
modules/local/kraken2/kraken2/environment.yml pypi
modules/nf-core/bwa/index/environment.yml pypi
modules/nf-core/bwa/mem/environment.yml pypi
modules/nf-core/checkm/lineagewf/environment.yml pypi
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/samtools/sort/environment.yml pypi
modules/nf-core/samtools/view/environment.yml pypi