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tomte

A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient

https://github.com/genomic-medicine-sweden/tomte

Science Score: 57.0%

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    Found 10 DOI reference(s) in README
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Last synced: 6 months ago · JSON representation ·

Repository

A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient

Basic Info
  • Host: GitHub
  • Owner: genomic-medicine-sweden
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Homepage:
  • Size: 81.5 MB
Statistics
  • Stars: 14
  • Watchers: 9
  • Forks: 4
  • Open Issues: 14
  • Releases: 10
Created about 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Codeowners

README.md

tomte tomte

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

Introduction

genomic-medicine-sweden/tomte is a bioinformatics best-practice analysis pipeline to analyse RNAseq from raredisease patients.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Pipeline summary

TrancriptOMe Total Evaluation (TOMTE):

  1. Trim reads (FASTP)
  2. Transcript quantification (Salmon)
  3. Align reads to the genome (STAR)
  4. Output junction tracks
  5. Output bigwig (UCSC wigToBigWig)
  6. Choice to subsample overrepresented regions (Samtools)
  7. Choice to downsample number of reads (Samtools)
  8. Detection of aberrant expression (DROP)
  9. Detection of aberrant splicing (DROP)
  10. Filter aberrant expression and aberrant splicing results
  11. Guided transcript assembly (StringTie)
  12. Filtering results of guided transcript assembly (GffCompare)
  13. To Call SNVs either path a or b can be followed. Path A will run by default a. Call SNVs
    1. (BCFtools Mpileups)
  14. b. Call SNVs
    1. Split cigar reads (SplitN Cigar Reads)
    2. Haplotype caller (Haplotype Caller)
    3. Variant filtration (Variant Filtration)
    4. BCFtools statistics (BCFtools stats)
  15. Allele Specific Read Counter (ASEReadCounter)
  16. Assess allelic imbalance (BootstrapAnn)
  17. Annotation (VEP)
  18. Alignment QC (Picard CollectRnaSeqMetrics)
  19. Present QCs (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.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv case,sample,fastq_1,fastq_2,strandedness case_id,sample_id,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,reverse

Each row represents a pair of fastq files (paired end).

-->

Now, you can run the pipeline using:

bash nextflow run genomic-medicine-sweden/tomte \ -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 and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

For more details about the output files and reports, please refer to the output documentation.

Credits

genomic-medicine-sweden/tomte was written by Clinical Genomics Stockholm, Sweden, with major contributions from Lucía Peña-Pérez, Anders Jemt, and Jesper Eisfeldt.

Additional contributors were Ramprasad Neethiraj, Felix Lenner, Jakob Willforss, Esmee ten Berk de Boer, Vadym Ivanchuk, and Mei Wu.

We thank the nf-core community for their extensive assistance in the development of this pipeline.

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 by opening an issue.

Citations

If you use genomic-medicine-sweden/tomte for your analysis, please cite it using the following doi: 10.5281/zenodo.10828946

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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: Genomic Medicine Sweden
  • Login: genomic-medicine-sweden
  • Kind: organization
  • Location: Sweden

Citation (CITATIONS.md) 

# genomic-medicine-sweden/tomte: 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

- [BCFtools](https://academic.oup.com/gigascience/article/10/2/giab008/6137722)

  > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008

- [UCSC tools](https://academic.oup.com/bioinformatics/article/26/17/2204/199001)

  > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351

- [SAMtools](https://academic.oup.com/gigascience/article/10/2/giab008/6137722)

  > Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008

- [EnsemblVEP](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4)

  > McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4

- [DROP](https://www.nature.com/articles/s41596-020-00462-5)

  > Yépez, V.A., Mertes, C., Müller, M.F. et al. Detection of aberrant gene expression events in RNA sequencing data. Nat Protoc 16, 1276–1296 (2021). doi:10.1038/s41596-020-00462-5

- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/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. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [FRASER](https://www.nature.com/articles/s41467-020-20573-7)

  > Mertes C, Scheller IF, Yépez VA, et al. Detection of aberrant splicing events in RNA-seq data using FRASER [published correction appears in Nat Commun. 2022 Jun 16;13(1):3474]. Nat Commun. 2021;12(1):529. Published 2021 Jan 22. doi:10.1038/s41467-020-20573-7

- [GATK](https://genome.cshlp.org/content/20/9/1297)

  > McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-1303. doi:10.1101/gr.107524.110

- [GffCompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml)

  > Pertea G and Pertea M. GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]. F1000Research 2020, 9:304 (https://doi.org/10.12688/f1000research.23297.1)

- [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.

- [OUTRIDER](https://www.sciencedirect.com/science/article/pii/S0002929718304014?via%3Dihub)

  > Brechtmann F, Mertes C, Matusevičiūtė A, et al. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data. Am J Hum Genet. 2018;103(6):907-917. doi:10.1016/j.ajhg.2018.10.025

- [picard-tools](http://broadinstitute.github.io/picard)

- [StringTie](http://ccb.jhu.edu/software/stringtie/)

  > Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. PMID: 25690850; PMCID: PMC4643835.

- [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/)

  > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/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. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

## 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.

GitHub Events

Total
  • Create event: 47
  • Release event: 3
  • Issues event: 37
  • Watch event: 3
  • Delete event: 38
  • Issue comment event: 112
  • Push event: 297
  • Pull request review event: 304
  • Pull request review comment event: 320
  • Pull request event: 98
  • Fork event: 1
Last Year
  • Create event: 47
  • Release event: 3
  • Issues event: 37
  • Watch event: 3
  • Delete event: 38
  • Issue comment event: 112
  • Push event: 297
  • Pull request review event: 304
  • Pull request review comment event: 320
  • Pull request event: 98
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 33
  • Total pull requests: 125
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 6
  • Total pull request authors: 5
  • Average comments per issue: 0.67
  • Average comments per pull request: 1.17
  • Merged pull requests: 98
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 14
  • Pull requests: 45
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 4
  • Average comments per issue: 0.93
  • Average comments per pull request: 1.02
  • Merged pull requests: 27
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Lucpen (28)
  • Jakob37 (20)
  • jemten (9)
  • A97paupic (2)
  • arvindsundaram (1)
  • fellen31 (1)
Pull Request Authors
  • Lucpen (166)
  • jemten (21)
  • fellen31 (5)
  • Jakob37 (4)
  • pbiology (2)
Top Labels
Issue Labels
enhancement (32) bug (20) question (3) Ready for review (2) documentation (1)
Pull Request Labels
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