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rnafusion

RNA-seq analysis pipeline for detection of gene-fusions

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

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.3%) to scientific vocabulary

Keywords

fusion fusion-genes gene-fusion nextflow nf-core pipeline rna rna-seq workflow

Keywords from Contributors

bioinformatics pipelines workflows epigenome metagenomics variant-calling dsl2 nf-test linting genomics
Last synced: 6 months ago · JSON representation ·

Repository

RNA-seq analysis pipeline for detection of gene-fusions

Basic Info
  • Host: GitHub
  • Owner: nf-core
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage: https://nf-co.re/rnafusion
  • Size: 22.9 MB
Statistics
  • Stars: 162
  • Watchers: 164
  • Forks: 117
  • Open Issues: 17
  • Releases: 17
Topics
fusion fusion-genes gene-fusion nextflow nf-core pipeline rna rna-seq workflow
Created over 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/rnafusion

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Get help on SlackFollow on TwitterFollow on MastodonWatch on YouTube

Introduction

nf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualiation document, a vcf data collection file, and html and tsv reports.

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website.

In rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from here.

Pipeline summary

nf-core/rnafusion metro map

Build references

--build_references triggers a parallel workflow to build references, which is a prerequisite to running the pipeline:

  1. Download ensembl fasta and gtf files
  2. Create STAR index
  3. Download Arriba references
  4. Download FusionCatcher references
  5. Download and build STAR-Fusion references
  6. Download Fusion-report DBs

Main workflow

  1. Input samplesheet check
  2. Concatenate fastq files per sample (cat)
  3. Reads quality control (FastQC)
  4. Optional trimming with fastp
  5. Arriba subworkflow
  6. STAR-fusion subworkflow
  7. Fusioncatcher subworkflow
  8. StringTie subworkflow
  9. Fusion-report
    • Merge all fusions detected by the selected tools with Fusion-report
  10. Post-processing and analysis of data
  11. Present QC for raw reads (MultiQC)
  12. Compress bam files to cram with samtools view

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.

As the reference building is computationally heavy (> 24h on HPC), it is recommended to test the pipeline with the -stub parameter (creation of empty files):

First, build the references:

bash nextflow run nf-core/rnafusion \ -profile <docker/singularity/.../institute> \ -profile test \ --outdir <OUTDIR>\ --build_references \ -stub

Then perform the analysis:

bash nextflow run nf-core/rnafusion \ -profile <docker/singularity/.../institute> \ -profile test \ --outdir <OUTDIR>\ -stub

[!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.

Notes:

  • Conda is not currently supported; run with singularity or docker.
  • Paths need to be absolute.
  • GRCh38 is the only supported reference.
  • Single-end reads are to be used as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp.

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

Pipeline output

To see the results of an example 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/rnafusion was written by Martin Proks (@matq007), Maxime Garcia (@maxulysse) and Annick Renevey (@rannick)

We thank the following people for their help 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 on the Slack #rnafusion channel (you can join with this invite).

Citations

If you use nf-core/rnafusion for your analysis, please cite it using the following doi: 10.5281/zenodo.3946477

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: 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/rnafusion: 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

- [Arriba](https://github.com/suhrig/arriba)

  > Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B, Toprak UH, Neumann O, Stenzinger A, Scholl C, Fröhling S, Brors B. Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Research. 2021 Mar 31;448-460. doi: 10.1101/gr.257246.119. Epub 2021 Jan 13. PubMed PMID: 33441414.

- [BEDOPS](https://bedops.readthedocs.io/en/latest/index.html) - convert2bed

  > Neph S, Scott Kuehn M, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012 May, 28 (14): 1919-1920. doi: 10.1093/bioinformatics/bts277, PubMed PMID: PMID: 22576172.

- [FastP](https://academic.oup.com/bioinformatics/article/34/17/i884/5093234)

  > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sept 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].

- [FusionCatcher](https://github.com/ndaniel/fusioncatcher)

  > Nicorici D, Satalan M, Edgren H, Kangaspeska S, Murumagi A, Kallioniemi O, Virtanen S, Kilkku O. FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data. BioRxiv, 2014 Nov. doi: 10.1101/011650.

- [FusionInspector](https://github.com/FusionInspector/FusionInspector)

  > Haas BJ, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson JT, Gillani R, Kasif S, Regev A. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Reports Methods. 2023 May 3:5, doi: 10.1016/j.crmeth.2023.100467, PMID: 37323575

- [Fusion-report](https://github.com/matq007/fusion-report)

  > Proks M, Genomic Profiling of a Comprehensive Nation-wide Collection of Childhood Solid Tumors, Master Thesis, Supervisors: Grøntved L, Díaz de Ståhl T, Nistér M, Ewels P, Garcia MU, Juhos S, University of Southern Denmark, 2019, unpublished.

- [GATK4](https://gatk.broadinstitute.org/hc/en-us)

  > Van der Auwera GA. Somatic variation discovery with GATK4. Proceedings of the American Association for Cancer Research Annual Meeting 2017. 2017 Apr 1-5. Cancer Res 2017;77(13 Suppl) doi:10.1158/1538-7445.AM2017-3590

- [MegaFusion](https://github.com/J35P312/MegaFusion)

- [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.

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

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [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.

- [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion)

  > Haas BJ, Dobin A, Li B, Stransky N, Pochet N, Regev A. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biology 2019 Oct;20,213. doi: 10.1186/s13059-019-1842-9

- [StringTie](https://ccb.jhu.edu/software/stringtie/index.shtml)
  > Shumate A, Wong B, Pertea G, Pertea M. Improved transcriptome assembly using a hybrid of long and short reads with StringTie. PLOS Computational Biology 18, 6 (2022), doi.org/10.1371/journal.pcbi.1009730

## 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
  • Issues event: 189
  • Watch event: 24
  • Delete event: 20
  • Issue comment event: 369
  • Push event: 380
  • Pull request review event: 347
  • Pull request review comment event: 294
  • Pull request event: 147
  • Fork event: 21
  • Create event: 34
Last Year
  • Issues event: 189
  • Watch event: 24
  • Delete event: 20
  • Issue comment event: 369
  • Push event: 380
  • Pull request review event: 347
  • Pull request review comment event: 294
  • Pull request event: 147
  • Fork event: 21
  • Create event: 34

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,325
  • Total Committers: 26
  • Avg Commits per committer: 50.962
  • Development Distribution Score (DDS): 0.45
Past Year
  • Commits: 317
  • Committers: 7
  • Avg Commits per committer: 45.286
  • Development Distribution Score (DDS): 0.114
Top Committers
Name Email Commits
Annick Renevey 4****k 729
Martin Proks m****k@g****m 335
MaxUlysse m****a@g****m 92
Rickard Hammarén r****n@s****e 46
nf-core-bot c****e@n****e 25
Praveen p****6@g****m 16
Oliver Ziff 4****f 13
Alexander Peltzer a****r@g****m 13
rannick a****y@h****e 11
Alexander Peltzer a****r@b****m 10
Eva Caceres e****s@s****e 9
brucemoran b****n@g****m 4
Matthias De Smet m****t@u****e 4
Alexander Peltzer a****r 4
Phil Ewels p****s@s****e 2
Ed Stone e****e@m****k 2
kevinmenden k****n@t****e 1
Chadi Saad c****d@h****m 1
Z_Wael z****s@g****m 1
Tobias Neumann t****t@g****m 1
Travis CI User t****s@e****g 1
Maxime Garcia m****a@s****e 1
Matthias De Smet 1****m 1
Matthias Stahl m****7@w****e 1
Simon Pearce 2****e 1
runner r****r@f****0 1
Committer Domains (Top 20 + Academic)
scilifelab.se: 4 example.org: 1 t-online.de: 1 mft.nhs.uk: 1 ugent.be: 1 boehringer-ingelheim.com: 1 hasta.scilifelab.se: 1 nf-co.re: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 200
  • Total pull requests: 195
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 58
  • Total pull request authors: 24
  • Average comments per issue: 1.33
  • Average comments per pull request: 1.46
  • Merged pull requests: 127
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 106
  • Pull requests: 90
  • Average time to close issues: 27 days
  • Average time to close pull requests: 6 days
  • Issue authors: 26
  • Pull request authors: 14
  • Average comments per issue: 0.76
  • Average comments per pull request: 1.38
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rannick (45)
  • nschcolnicov (26)
  • atrigila (20)
  • apeltzer (13)
  • fevac (10)
  • delfiterradas (5)
  • tkcaccia (5)
  • maressyl (4)
  • artgenko (4)
  • jsangalang (3)
  • wudustan (3)
  • mschubert (3)
  • bounlu (3)
  • dslarm (2)
  • shwcha9 (2)
Pull Request Authors
  • rannick (90)
  • atrigila (22)
  • nf-core-bot (20)
  • nvnieuwk (15)
  • apeltzer (9)
  • delfiterradas (9)
  • alanmmobbs93 (5)
  • fevac (5)
  • asp8200 (2)
  • efgstone (2)
  • SPPearce (2)
  • matthdsm (2)
  • KuthuruTejaswini (1)
  • nschcolnicov (1)
  • HaidYi (1)
Top Labels
Issue Labels
bug (80) wontfix (5) good first issue (5) feature-request (4) documentation (3) fusion-report (2) waiting (1)
Pull Request Labels
waiting-for-review (21) bug (3) WIP (2) waiting (1)

Dependencies

.github/workflows/awsfulltest.yml actions
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • nf-core/tower-action v3 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v2 composite
.github/workflows/linting.yml actions
  • actions/checkout v2 composite
  • actions/setup-node v2 composite
  • actions/setup-python v3 composite
  • actions/upload-artifact v2 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
containers/arriba/Dockerfile docker
  • nfcore/base 1.9 build
containers/ericscript/Dockerfile docker
  • nfcore/base 1.9 build
containers/fusioncatcher/Dockerfile docker
  • ubuntu 18.04 build
containers/pizzly/Dockerfile docker
  • nfcore/base 1.9 build
containers/squid/Dockerfile docker
  • nfcore/base 1.9 build
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
modules/local/arriba/download/meta.yml cpan
modules/local/arriba/visualisation/meta.yml cpan
modules/local/convert2bed/meta.yml cpan
modules/local/fusioncatcher/detect/meta.yml cpan
modules/local/fusioncatcher/download/meta.yml cpan
modules/local/fusioninspector/meta.yml cpan
modules/local/fusionreport/detect/meta.yml cpan
modules/local/fusionreport/download/meta.yml cpan
modules/local/kallisto/quant/meta.yml cpan
modules/local/megafusion/meta.yml cpan
modules/local/picard/collectrnaseqmetrics/meta.yml cpan
modules/local/pizzly/detect/meta.yml cpan
modules/local/reformat/meta.yml cpan
modules/local/squid/annotate/meta.yml cpan
modules/local/squid/detect/meta.yml cpan
modules/local/starfusion/build/meta.yml cpan
modules/local/starfusion/detect/meta.yml cpan
modules/local/starfusion/download/meta.yml cpan
modules/local/uscs/custom_gtftogenepred/meta.yml cpan
modules/nf-core/arriba/meta.yml cpan
modules/nf-core/cat/cat/meta.yml cpan
modules/nf-core/cat/fastq/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastp/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/gatk4/bedtointervallist/meta.yml cpan
modules/nf-core/gatk4/createsequencedictionary/meta.yml cpan
modules/nf-core/kallisto/index/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/picard/collectwgsmetrics/meta.yml cpan
modules/nf-core/picard/markduplicates/meta.yml cpan
modules/nf-core/qualimap/rnaseq/meta.yml cpan
modules/nf-core/samtools/faidx/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/samtools/view/meta.yml cpan
modules/nf-core/star/align/meta.yml cpan
modules/nf-core/star/genomegenerate/meta.yml cpan
modules/nf-core/stringtie/merge/meta.yml cpan
modules/nf-core/stringtie/stringtie/meta.yml cpan
containers/arriba/environment.yml pypi
containers/ericscript/environment.yml pypi
containers/pizzly/environment.yml pypi
containers/squid/environment.yml pypi
pyproject.toml pypi