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ribomsqc

QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis

https://github.com/nf-core/ribomsqc

Science Score: 57.0%

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    Found 6 DOI reference(s) in README
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Keywords

nextflow nf-core pipeline workflow
Last synced: 6 months ago · JSON representation ·

Repository

QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis

Basic Info
  • Host: GitHub
  • Owner: nf-core
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Homepage: https://nf-co.re/ribomsqc
  • Size: 326 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Topics
nextflow nf-core pipeline workflow
Created about 1 year ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/ribomsqc

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Introduction

nf-core/ribomsqc is a bioinformatics pipeline that processes RAW files from mass spectrometry instruments, converts them to mzML format, extracts XICs for selected analytes, generates plots, and summarizes outputs via MultiQC. It is tailored for quality control of ribonucleoside analysis.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

  1. Prepare a samplesheet with your input data, for example:

csv title="samplesheet.csv" id,raw_file Day_5,path/to/Day_5.raw

For more information, see the usage docs on required samplesheet.csv columns.

  1. Prepare an analytes TSV file (e.g. qcn1.tsv) with your compounds and theoretical retention times. The TSV must have exactly these columns and format:

tsv short_name long_name mz_M0 mz_M1 mz_M2 ms2_mz rt_teoretical C Cytidine 50 μg/mL 244.0928 112.0505 555 U Uridine 25 μg/mL 245.0768 113.0346 1566 m3C 3-Methylcytidine methosulfate 100 μg/mL 258.1084 126.0662 508 m5C 5-Methylcytidine 100 μg/mL 258.1084 126.0662 655 Cm 2-O-Methylcytidine 20 μg/mL 258.1084 112.0505 883 m5U 5-Methyluridine 50 μg/mL 259.0925 127.0502 1866 I Inosine 25 μg/mL 269.088 137.0458 1741 m1A 1-Methyladenosine 25 μg/mL 282.1197 150.0774 523 G Guanosine 25 μg/mL 284.0989 152.0567 1726 m7G 7-Methylguanosine 25 μg/mL 298.1146 166.0723 554

[!NOTE] Replace only the values in the rt_teoretical column with your own retention times (in seconds) for each compound.

  1. Run the pipeline:

bash nextflow run nf-core/ribomsqc \ --input samplesheet.csv \ --analytes_tsv qcn1.tsv \ --analyte all \ --rt_tolerance 120 \ --mz_tolerance 7 \ --ms_level 1 \ --outdir results \ -profile singularity

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option.

For more information, see the usage docs and parameters.

Pipeline output

See results page for example output and output docs.

Credits

nf-core/ribomsqc was originally written by Roger Olivella.

Contributions and Support

For help, visit Slack #ribomsqc or see contributing guide.

Citations

See CITATIONS.md for tool references.

Ewels PA et al. (2020) The nf-core framework. Nat Biotechnol. doi:10.1038/s41587-020-0439-x

Owner

  • Name: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/ribomsqc: 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

- [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser#thermorawfileparser)

  > Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y: ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion [PMID 31755270].

- [MSnbase - Bioconductor package](https://bioconductor.org/packages/release/bioc/html/MSnbase.html)

  > Gatto L, Lilley K (2012). “MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.” _Bioinformatics_, 28, 288–289.

  > Gatto L, Gibb S, Rainer J (2020). “MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data.” _bioRxiv_.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. _Bioinformatics_, 32(19), 3047–3048. doi: [10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354). PubMed PMID: [27312411](https://pubmed.ncbi.nlm.nih.gov/27312411/)

## 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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