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nf-core-phiflow

https://github.com/icaromsc/nf-core-phiflow

Science Score: 31.0%

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    Found CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 10 DOI reference(s) in README
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    Low similarity (10.5%) to scientific vocabulary

Keywords

metagenomics metatranscriptomics nextflow-pipeline rnaseq
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: icaromsc
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage:
  • Size: 2.26 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
metagenomics metatranscriptomics nextflow-pipeline rnaseq
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

nf-core/phiflow nf-core/phiflow

AWS CICite with Zenodo

Nextflow run with conda run with docker run with singularity Launch on Nextflow Tower

Get help on SlackFollow on TwitterFollow on MastodonWatch on YouTube

Introduction

nf-core/phiflow is a bioinformatics pipeline that simultaneously characterize the microbial composition and host gene expression RNA sequencing samples. Given a list of samples from raw reads as input data (FASTQ) the pipeline performs several steps to produce two data matrices: Host gene expression matrix and Microbial composition matrix. These data matrices can help researchers to investigate the host transcriptome response under the presence of identified microbes and the association of microbial presence with specific host gene modules.

phiflow Overview

  1. Read QC (fastp)
  2. Read alignment to the human host genome (STAR)
  3. Infer library strandedness (RSeQC)
  4. Quantify host gene expression (subread:featureCounts)
  5. Taxonomic profiling of host unmapped reads (Kraken2)
  6. Calculate confidence scores from Kraken2 taxonomic profiling (Conifer)
  7. Present summary of all previous processing steps (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.

Now, you can run the pipeline using:

bash nextflow run nf-core/phiflow \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --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.

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

Pipeline output

To see the the results of a 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/phiflow was originally written by Icaro Castro.

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

Robert A. Petit III @rpetit3 <!-- TODO nf-core: If applicable, make list of people who have also contributed -->

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 #phiflow 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: Ícaro M. S. Castro
  • Login: icaromsc
  • Kind: user
  • Location: Sao Paulo, Brazil
  • Company: University of São Paulo

Computational Biologist. PhD candidate at University of Sao Paulo.

Citation (CITATIONS.md) 

# nf-core/phiflow: 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

- [fastp](https://pubmed.ncbi.nlm.nih.gov/30423086/)
  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PMID: 30423086; PMCID: PMC6129281.

- [STAR](https://www.ncbi.nlm.nih.gov/pubmed/23104886/)
  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905.

- [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)
  > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PMID: 22743226.

- [subread:featurecounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
  > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PMID: 24227677.

- [Kraken2](https://pubmed.ncbi.nlm.nih.gov/31779668/)
  > Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019 Nov 28;20(1):257. doi: 10.1186/s13059-019-1891-0. PMID: 31779668; PMCID: PMC6883579.

- [Conifer](https://github.com/ivarz/conifer)

- [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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