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clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

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

Science Score: 77.0%

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
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 9 committers (22.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

clip clip-seq nextflow nf-core peak-calling pipeline rna-rbp-interactions workflow
Last synced: 6 months ago · JSON representation ·

Repository

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

Basic Info
  • Host: GitHub
  • Owner: nf-core
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage: https://nf-co.re/clipseq
  • Size: 64.8 MB
Statistics
  • Stars: 24
  • Watchers: 131
  • Forks: 40
  • Open Issues: 46
  • Releases: 1
Topics
clip clip-seq nextflow nf-core peak-calling pipeline rna-rbp-interactions workflow
Created over 5 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/clipseq

GitHub Actions CI Status GitHub Actions Linting Status Nextflow DOI

install with bioconda Docker Get help on Slack

Introduction

nf-core/clipseq is a bioinformatics best-practice analysis pipeline for CLIP (cross-linking and immunoprecipitation) sequencing data analysis to study RNA-protein interactions.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Pipeline Summary

By default, the pipeline currently performs the following:

  1. Adapter and quality trimming (Cutadapt)
  2. Pre-mapping to e.g. rRNA and tRNA sequences (Bowtie 2)
  3. Genome mapping (STAR)
  4. UMI-based deduplication (UMI-tools)
  5. Crosslink identification (BEDTools)
  6. Bedgraph coverage track generation (BEDTools)
  7. Peak calling (multiple options):
    • iCount
    • Paraclu
    • PureCLIP
    • Piranha
  8. Motif detection (DREME)
  9. Quality control:
    • Sequencing quality control (FastQC)
    • Library complexity (Preseq)
    • Regional distribution (RSeQC)
  10. Overall pipeline run and QC summaries and peak calling comparisons (MultiQC)

Quick Start

  1. Install nextflow

  2. Install any of Docker, Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs)

  3. Download the pipeline and test it on a minimal dataset with a single command:

    bash nextflow run nf-core/clipseq -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>

    Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

  4. Start running your own analysis!

    bash nextflow run nf-core/clipseq -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '[path to design file]' --fasta '[path to genome FASTA]'

See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/clipseq pipeline comes with documentation about the pipeline: usage and output.

Credits

nf-core/clipseq was originally written by Charlotte West (@charlotte-west) and Anob Chakrabarti (@amchakra) from Luscombe Lab at The Francis Crick Institute, London, UK.

It started life in April 2020 as a Nextflow DSL2 Luscombe Lab (@luslab) lockdown hackathon day and we thank all the lab members for their early contributions.

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 #clipseq channel (you can join with this invite).

Citations

If you use nf-core/clipseq for your analysis, please cite it using the following doi: 10.5281/zenodo.4723016

References of tools and data used in this pipeline can be found in CITATIONS.md

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/clipseq: 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

* [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)
  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

* [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.

* [preseq](https://pubmed.ncbi.nlm.nih.gov/23435259/)
  > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.

* [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. PubMed PMID: 22743226.

* [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.

* [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.

* [Cutadapt](http://journal.embnet.org/index.php/embnetjournal/article/view/200)
  > Martin, M., 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), p.10.

* [Bowtie2](https://pubmed.ncbi.nlm.nih.gov/22388286/)
  > Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923. PMID: 22388286; PMCID: PMC3322381.

* [Subread](https://pubmed.ncbi.nlm.nih.gov/23558742/)
  > Liao Y, Smyth GK, Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013 May 1;41(10):e108. doi: 10.1093/nar/gkt214. Epub 2013 Apr 4. PMID: 23558742; PMCID: PMC3664803.

* [iCount](https://icount.readthedocs.io/en/latest/#)
  > Curk et al. (2019) iCount: protein-RNA interaction iCLIP data analysis (in preparation).

* [PureCLIP](https://pubmed.ncbi.nlm.nih.gov/29284540/)
  > Krakau S, Richard H, Marsico A. PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. Genome Biol. 2017 Dec 28;18(1):240. doi: 10.1186/s13059-017-1364-2. PMID: 29284540; PMCID: PMC5746957.

* [Piranha](https://pubmed.ncbi.nlm.nih.gov/23024010/)
  > Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. Site identification in high-throughput RNA-protein interaction data. Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28. PMID: 23024010; PMCID: PMC3509493.

* [Paraclu](https://pubmed.ncbi.nlm.nih.gov/18032727/)
  > Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Genome Res. 2008 Jan;18(1):1-12. doi: 10.1101/gr.6831208. Epub 2007 Nov 21. PMID: 18032727; PMCID: PMC2134772.

* [Meme](https://pubmed.ncbi.nlm.nih.gov/19458158/)
  > Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8. doi: 10.1093/nar/gkp335. Epub 2009 May 20. PMID: 19458158; PMCID: PMC2703892.

* [R](https://www.r-project.org/)
  > R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

* [Pigz](https://zlib.net/pigz/)

## 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.

* [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.

GitHub Events

Total
  • Create event: 3
  • Issues event: 29
  • Watch event: 4
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 27
  • Push event: 23
  • Pull request review comment event: 1
  • Pull request review event: 2
  • Pull request event: 42
  • Fork event: 17
Last Year
  • Create event: 3
  • Issues event: 29
  • Watch event: 4
  • Delete event: 2
  • Member event: 1
  • Issue comment event: 27
  • Push event: 23
  • Pull request review comment event: 1
  • Pull request review event: 2
  • Pull request event: 42
  • Fork event: 17

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 391
  • Total Committers: 9
  • Avg Commits per committer: 43.444
  • Development Distribution Score (DDS): 0.581
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nobby Chakrabarti a****i@c****k 164
Charlotte West c****t@o****p 117
Charlotte West c****t@c****k 81
drpatelh d****l@g****m 18
nf-core-bot c****e@n****e 6
charlotte-west 5****t 2
Phil Ewels p****s@s****e 1
Harshil Patel d****h 1
Charlotte Capitanchik C****e 1
Committer Domains (Top 20 + Academic)
crick.ac.uk: 2 scilifelab.se: 1 nf-co.re: 1 oist.jp: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 32
  • Total pull requests: 78
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 1 month
  • Total issue authors: 10
  • Total pull request authors: 12
  • Average comments per issue: 0.78
  • Average comments per pull request: 0.58
  • Merged pull requests: 44
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 25
  • Pull requests: 16
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 21 days
  • Issue authors: 5
  • Pull request authors: 8
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.75
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • CharlotteAnne (29)
  • iraiosub (4)
  • kkuret (4)
  • amchakra (2)
  • adomingues (2)
  • tbrittoborges (1)
  • JohnRachid (1)
  • maxulysse (1)
  • mohamedbahru (1)
  • MelinaKlostermann (1)
  • marc-jones (1)
  • gl9797 (1)
  • apeltzer (1)
  • eeb74 (1)
  • neusmf (1)
Pull Request Authors
  • nf-core-bot (30)
  • amchakra (18)
  • charlotte-west (16)
  • neusmf (8)
  • CharlotteAnne (5)
  • drpatelh (5)
  • iraiosub (4)
  • ewels (3)
  • JDocherty67 (2)
  • vecerkovakaterina (2)
  • chris-cheshire (2)
  • SimranChhabria (1)
  • serjisa (1)
  • SimonDMurray (1)
  • Chromojones (1)
Top Labels
Issue Labels
enhancement (24) bug (16) documentation (1)
Pull Request Labels
enhancement (4) bug (2) documentation (1)

Dependencies

.github/workflows/awsfulltest.yml actions
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/awstest.yml actions
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • technote-space/get-diff-action v4 composite
.github/workflows/linting.yml actions
  • actions/checkout v2 composite
  • actions/checkout v1 composite
  • actions/setup-node v1 composite
  • actions/setup-python v1 composite
  • actions/upload-artifact v2 composite
  • mshick/add-pr-comment v1 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
.github/workflows/push_dockerhub_dev.yml actions
  • actions/checkout v2 composite
.github/workflows/push_dockerhub_release.yml actions
  • actions/checkout v2 composite
Dockerfile docker
  • nfcore/base 1.13.3 build
environment.yml conda
  • bedtools 2.29.2.*
  • bowtie2 2.4.2.*
  • cutadapt 3.0.*
  • fastqc 0.11.9.*
  • icount 2.0.0.*
  • markdown 3.1.1.*
  • meme 5.1.1.*
  • multiqc 1.9.*
  • paraclu 9.*
  • perl 5.26.2.*
  • pigz 2.3.4.*
  • piranha 1.2.1.*
  • preseq 2.0.3.*
  • pureclip 1.3.1.*
  • pygments 2.5.2.*
  • pymdown-extensions 6.0.*
  • python 3.7.3.*
  • rseqc 4.0.0.*
  • samtools 1.11.*
  • star 2.6.1d.*
  • subread 2.0.1.*
  • umi_tools 1.1.1.*