nf-genomeresolvedmetagenomics
A nextflow pipeline to perform genome resolved metagenomics
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A nextflow pipeline to perform genome resolved metagenomics
Basic Info
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README.md
genomeresolvedmetagenomics
Introduction
genomeresolvedmetagenomics is a Nextflow DSL2 pipeline written by Matt Olm, primarily for personal use. It was built using the nf-core framework and nf-core suite of tools, but it does not conform to the nf-core overarching style and thus is not available on the nf-core website. I may update this pipeline to conform and upload it there someday.
Pipeline summary
Unlike nf-core pipelines, this pipeline is structured around entry points. This allows you to easily run some, but not other, pipelines. In pracice each entry is a sub-workflow. Below is a quick summary of the currently available entry points:
PREPROCESSREADS
Takes an input datasheet listing paired reads and runs fastqc to evaluate initial read quality, fastp to trim reads and remove adapters, bowtie2 against the human genome to remove human reads (optional), and a small script at the end to summarize the number of reads and read pairs remaining at the end.
The --input parameter must but a .csv file with the columns "sample, "fastq1", and "fastq2" (like this - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheettestillumina_sispa.csv). The locations of the reads can be local, on S3, or on the web
PROFILE
Takes an input datasheet listing paired reads (you probably want trimmed paired reads, like those you get from PREPROCESSREADS!), maps reads to the provides fasta file using bowtie2, and profiles the read mapping using inStrain.
The --input parameter has the same rules as above
Quick Start
Install
Nextflow(>=21.10.3)Install
Docker- there are other alternitives that you can use, but I prefer DockerTest the pipeline on the provided dataset with a single command:
```console $ nextflow pull https://github.com/MrOlm/nf-genomeresolvedmetagenomics
$ nextflow run https://github.com/MrOlm/nf-genomeresolvedmetagenomics -profile test,docker -entry PREPROCESSREADS --outdir testout/ ```
- Start running your own analysis!
Example run for PREPROCESSREADS:
console
nextflow run https://github.com/MrOlm/nf-genomeresolvedmetagenomics -entry PREPROCESSREADS --input input_samplesheet_v3.csv -with-report test_report.html --outdir results_1/ -resume
Example run for PROFILE:
console
nextflow run https://github.com/MrOlm/nf-genomeresolvedmetagenomics -entry PROFILE --input input_samplesheet_v5.csv -with-report rest_report.html --outdir results_2 -profile docker --fasta transcriptome_chopped_num.fa --stb_file transcriptome.stb -resume
Documentation
Access a list of accepted parameters by running:
console
nextflow run https://github.com/MrOlm/nf-genomeresolvedmetagenomics --help
bin documentation- docs/bin_README.md
Credits, Contributions, and Support
genomeresolvedmetagenomics was written by Matt Olm
If you would like to contribute to this pipeline please reach out to me via email or by posting an issue or pull request on this Github page
While this is not an nf-core pipeline it is built on the back of the nf-core framework. 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: Matt Olm
- Login: MrOlm
- Kind: user
- Location: San Francisco, CA
- Company: Stanford University
- Website: https://mrolm.github.io/
- Twitter: MattagenOlmics
- Repositories: 8
- Profile: https://github.com/MrOlm
Postdoc in Justin Sonnenburg's lab at Stanford
Citation (CITATIONS.md)
# nf-core/genomeresolvedmetagenomics: 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.
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