hicar
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
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Repository
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
Basic Info
- Host: GitHub
- Owner: nf-core
- License: mit
- Language: Nextflow
- Default Branch: dev
- Homepage: https://nf-co.re/hicar
- Size: 34.7 MB
Statistics
- Stars: 11
- Watchers: 108
- Forks: 7
- Open Issues: 9
- Releases: 1
Topics
Metadata Files
README.md
Introduction
nf-core/hicar is a bioinformatics best-practice analysis pipeline for HiC on Accessible Regulatory DNA (HiCAR) data, a robust and sensitive assay for simultaneous measurement of chromatin accessibility and cis-regulatory chromatin contacts. Unlike the immunoprecipitation-based methods such as HiChIP, PlAC-seq and ChIA-PET, HiCAR does not require antibodies. HiCAR utilizes a Transposase-Accessible Chromatin assay to anchor the chromatin interactions. HiCAR is a tool to study chromatin interactions for low input samples and samples with no available antibodies.
The pipeline can also handle the experiment of HiChIP, ChIA-PET, and PLAC-Seq. It will ask user to input the peak file for the anchor peaks.
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!
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.
Pipeline summary
- Read QC (
FastQC) - Trim reads (
cutadapt) - Map reads (
bwa mem) - Filter reads (
pairtools) - Quality analysis (
pairsqc) - Create cooler files (
cooler) - Call peaks for ATAC reads (R2 reads) (
MACS2). - Call A/B compartments (
cooltools,homer, etc.) - Call TADs (
HiCExplorer,homer, etc.) - Find genomic interaction loops (
MAPS,HiCDCPlus, Peakachu, etc.) - Aggregate peak analysis (
HiCExplorer,Juicer_tools, etc.) - Call HiPeak (high resolution analysis, time consuming, motif analysis)
- Differential analysis (
diffHic, etc.) - Annotate genomic interaction loops (
ChIPpeakAnno) - Visualization (.mcools files
cooler, .hic filesJuicer_tools, and circos filescircos) - Pipeline reporting (
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 testbefore running the workflow on actual data.
First, prepare a samplesheet with your input data that looks as follows:
samplesheet.csv:
csv
group,replicate,fastq_1,fastq_2
CONTROL,1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Now, you can run the pipeline using:
console
nextflow run nf-core/hicar \
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
--input samplesheet.csv \ # Input data
--qval_thresh 0.01 \ # Cut-off q-value for MACS2
--genome GRCh38 \ # Genome Reference
--mappability /path/mappability/bigWig/file # Provide mappability to avoid memory intensive calculation
Warning: Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow 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
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/hicar was originally written by Jianhong Ou, Yu Xiang, and Yarui Diao.
We thank the following people for their extensive assistance in the development of this pipeline: Luke Zappia, James A. Fellows Yates, Phil Ewels, Mahesh Binzer-Panchal and Friederike Hanssen.
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 #hicar channel (you can join with this invite).
Citations
If you use nf-core/hicar for your analysis, please cite it using the following doi: 10.5281/zenodo.6515312
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
- Website: http://nf-co.re
- Twitter: nf_core
- Repositories: 84
- Profile: https://github.com/nf-core
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Citation (CITATIONS.md)
# nf-core/hicar: Citations ## [HiC on Accessible Regulatory DNA (HiCAR)](https://doi.org/10.1016/j.molcel.2022.01.023) > Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Mol Cell. 2022 Mar 17;82(6):1225-1238.e6. doi: 10.1016/j.molcel.2022.01.023. Epub 2022 Feb 22. PMID: 35196517; PMCID: PMC8934281. ## [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 - [BWA](https://www.ncbi.nlm.nih.gov/pubmed/19451168/) > Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PubMed PMID: 19451168; PubMed Central PMCID: PMC2705234. - [BEDTools](https://www.ncbi.nlm.nih.gov/pubmed/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. - [ChIPpeakAnno](https://pubmed.ncbi.nlm.nih.gov/20459804/) > Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237. PMID: 20459804; PMCID: PMC3098059. - [clusterProfiler](https://pubmed.ncbi.nlm.nih.gov/22455463/) > Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28. PMID: 22455463; PMCID: PMC3339379. - [circos](https://pubmed.ncbi.nlm.nih.gov/19541911/) > Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009 Sep;19(9):1639-45. doi: 10.1101/gr.092759.109. Epub 2009 Jun 18. PMID: 19541911; PMCID: PMC2752132. - [cooler](https://pubmed.ncbi.nlm.nih.gov/31290943/) > Abdennur N, Mirny LA. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020 Jan 1;36(1):311-316. doi: 10.1093/bioinformatics/btz540. PMID: 31290943. - [cooltools](https://doi.org/10.5281/zenodo.5214125) - [diffhic](https://pubmed.ncbi.nlm.nih.gov/26283514/) > Lun AT, Smyth GK. diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics. 2015 Aug 19;16:258. doi: 10.1186/s12859-015-0683-0. PMID: 26283514; PMCID: PMC4539688. - [edgeR](https://pubmed.ncbi.nlm.nih.gov/19910308/) > Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. PMID: 19910308; PMCID: PMC2796818. - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. - [GenMap](https://pubmed.ncbi.nlm.nih.gov/32246826/) > Pockrandt C, Alzamel M, Iliopoulos CS, Reinert K. GenMap: ultra-fast computation of genome mappability. Bioinformatics. 2020 Jun 1;36(12):3687-3692. doi: 10.1093/bioinformatics/btaa222. PMID: 32246826; PMCID: PMC7320602. - [HiC-DC+](https://doi.org/10.1038/s41467-021-23749-x) > Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS. HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Nat Commun. 2021 Jun 7;12(1):3366. doi: 10.1038/s41467-021-23749-x. PMID: 34099725; PMCID: PMC8184932. - [HiCExplorer](https://pubmed.ncbi.nlm.nih.gov/29335486/) > Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w. PMID: 29335486; PMCID: PMC5768762. - [Homer](http://homer.ucsd.edu/homer/) > Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432 - [igv.js](https://pubmed.ncbi.nlm.nih.gov/22517427/) > Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013 Mar;14(2):178-92. doi: 10.1093/bib/bbs017. Epub 2012 Apr 19. PMID: 22517427; PMCID: PMC3603213. - [Juicer_tools](https://pubmed.ncbi.nlm.nih.gov/27467249/) > Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016 Jul;3(1):95-8. doi: 10.1016/j.cels.2016.07.002. PMID: 27467249; PMCID: PMC5846465. - [MACS2](https://www.ncbi.nlm.nih.gov/pubmed/18798982/) > Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. PubMed PMID: 18798982; PubMed Central PMCID: PMC2592715. - [MAPS](https://pubmed.ncbi.nlm.nih.gov/30986246/) > Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLoS Comput Biol. 2019 Apr 15;15(4):e1006982. doi: 10.1371/journal.pcbi.1006982. PMID: 30986246; PMCID: PMC6483256. - [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. - [pairsqc](https://github.com/4dn-dcic/pairsqc) - [pairtools](https://github.com/open2c/pairtools) - [peakachu](https://doi.org/10.1038/s41467-020-17239-9) > Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Ruan Y, Yue F. A supervised learning framework for chromatin loop detection in genome-wide contact maps. Nat Commun. 2020 Jul 9;11(1):3428. doi: 10.1038/s41467-020-17239-9. PMID: 32647330; PMCID: PMC7347923. - [SAMtools](https://www.ncbi.nlm.nih.gov/pubmed/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. - [trackViewer](https://pubmed.ncbi.nlm.nih.gov/31133757/) > Ou J, Zhu LJ. trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data. Nat Methods. 2019 Jun;16(6):453-454. doi: 10.1038/s41592-019-0430-y. PMID: 31133757. - [UCSC tools](https://www.ncbi.nlm.nih.gov/pubmed/20639541/) > 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. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891. ## 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: 1
- Watch event: 5
- Issue comment event: 6
- Push event: 4
- Pull request review comment event: 3
- Pull request review event: 1
- Pull request event: 10
- Fork event: 2
- Create event: 4
Last Year
- Issues event: 1
- Watch event: 5
- Issue comment event: 6
- Push event: 4
- Pull request review comment event: 3
- Pull request review event: 1
- Pull request event: 10
- Fork event: 2
- Create event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| JIANHONG OU | j****g | 439 |
| nf-core-bot | c****e@n****e | 12 |
| James A. Fellows Yates | j****3@g****m | 5 |
| Phil Ewels | p****s@s****e | 3 |
| Yu Xiang | y****h@g****m | 1 |
| jianhong | j****u@g****m | 1 |
| Rike | f****n@q****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 6
- Total pull requests: 99
- Average time to close issues: 3 months
- Average time to close pull requests: 9 days
- Total issue authors: 5
- Total pull request authors: 5
- Average comments per issue: 1.33
- Average comments per pull request: 1.81
- Merged pull requests: 71
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 19 days
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.4
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- shangguandong1996 (2)
- Adeel3Dgenomics (1)
- nvnieuwk (1)
- nf-core-bot (1)
- Rhine86 (1)
- ILM-MLOlab (1)
- realzhang (1)
- luciazifcakova (1)
Pull Request Authors
- jianhong (76)
- nf-core-bot (26)
- ewels (7)
- jfy133 (2)
- FriederikeHanssen (1)
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Dependencies
- nf-core/tower-action v3 composite
- nf-core/tower-action v3 composite
- mshick/add-pr-comment v1 composite
- actions/checkout v2 composite
- actions/checkout v2 composite
- actions/setup-node v2 composite
- actions/setup-python v1 composite
- actions/upload-artifact v2 composite
- dawidd6/action-download-artifact v2 composite
- marocchino/sticky-pull-request-comment v2 composite
- actions/stale v7 composite
- actions/checkout v3 composite
- actions/setup-node v3 composite