nf-core pipeline · atac, atac-seq, hic
nf-core/hicar
A Nextflow pipeline for simultaneous profiling of chromatin accessibility and cis-regulatory chromatin interactions.
What nf-core/hicar is
nf-core/hicar is a bioinformatics analysis pipeline designed for HiC on Accessible Regulatory DNA (HiCAR) data. HiCAR is a multi-omic assay that simultaneously captures chromatin accessibility and cis-regulatory chromatin contacts. Unlike immunoprecipitation-dependent techniques such as HiChIP, PLAC-seq, and ChIA-PET, HiCAR does not require antibodies and instead uses an assay for transposase-accessible chromatin to anchor contacts, making it well-suited for low-input samples.
Beyond native HiCAR experiments, the pipeline can also analyse datasets from HiChIP, ChIA-PET, and PLAC-seq when supplied with user-provided anchor peak files. It was originally developed by Jianhong Ou, Yu Xiang, and Yarui Diao using Nextflow DSL2, employing software containers for each analytical process to ensure computational reproducibility.
What the pipeline does
Sequencing reads undergo initial quality checks with FastQC and adapter trimming via cutadapt. Reads are aligned to the reference genome using BWA-MEM, after which pairtools filters valid interaction pairs and pairsqc evaluates library quality. Contact matrices are compiled into multiresolution cooler files. For HiCAR assays, MACS2 calls accessible chromatin peaks from the R2 reads to establish anchor positions.
Downstream structural analysis includes compartment identification using cooltools or HOMER, topologically associating domain (TAD) boundary detection with HiCExplorer or HOMER, and interaction loop calling with MAPS, HiCDCPlus, or Peakachu. The workflow also performs aggregate peak analysis, high-resolution HiPeak calling with motif analysis, differential contact detection via diffHic, and peak annotation using ChIPpeakAnno. Results are visualised as .mcool, .hic, and circos files, with summary metrics compiled into a MultiQC report.
Key facts
- Pipeline framework
- Nextflow DSL2
- Original developers
- Jianhong Ou, Yu Xiang, and Yarui Diao
- Latest release
- 1.0.0 (2022-05-03)
- Input formats
- FASTQ (paired-end or single-end), CSV samplesheet, reference genome FASTA
- Accessibility peak caller
- MACS2
- Loop calling tools
- MAPS, HiCDCPlus, Peakachu
- Differential analysis
- diffHic
- Visualisation formats
- .mcool (cooler), .hic (Juicer_tools), Circos
What you can use it for
- HiCAR assay processing
- Simultaneously identifies transposase-accessible open chromatin regions and long-range regulatory chromatin loops from HiCAR sequencing libraries without antibody enrichment.
- Antibody-guided conformation analysis
- Processes HiChIP, ChIA-PET, and PLAC-seq sequencing data by supplying pre-defined genomic anchor peaks to guide interaction calling.
- Higher-order genome organisation mapping
- Identifies A/B genomic compartments and topologically associating domains (TADs) across sample groups.
- Comparative chromatin contact analysis
- Discovers statistically significant differences in genomic interaction frequencies across biological conditions and replicates using diffHic.
Run it here
The research agent runs nf-core/hicar with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Supports both antibody-free HiCAR assays and targeted antibody assays such as HiChIP, PLAC-seq, and ChIA-PET.
- Integrates multiple complementary chromatin interaction callers, including MAPS, HiCDCPlus, and Peakachu.
- Exports interaction data in widely used visualisation formats including cooler (.mcool), Juicer (.hic), and circos files.
- Utilises containerised Nextflow DSL2 modules for reproducible deployment across diverse computing platforms.
Watch out for
- Processing non-HiCAR datasets like HiChIP, ChIA-PET, or PLAC-seq requires the user to supply external anchor peak files.
- High-resolution interaction and motif analysis using HiPeak is computationally intensive and time-consuming.
- Omitting a pre-calculated mappability track necessitates memory-intensive on-the-fly calculations.
Questions
Can I run nf-core/hicar without my own cluster?
The research agent runs nf-core/hicar with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/hicar under?
MIT, like every nf-core pipeline.
Can this pipeline be used for standard HiChIP or ChIA-PET experiments?
Yes. The pipeline supports HiChIP, ChIA-PET, and PLAC-seq data, though users must provide an external peak file to designate the anchor regions.
How are chromatin accessibility peaks identified in HiCAR data?
MACS2 is used to call peaks directly from the R2 sequencing reads, which correspond to the transposase-accessible chromatin fragments.
How can high memory usage be avoided during execution?
Users can provide a pre-computed mappability track in bigWig format via the pipeline options, avoiding resource-heavy runtime mappability calculations.
Which software tools identify chromatin interaction loops?
The workflow can identify genomic interaction loops using MAPS, HiCDCPlus, and Peakachu.
How to cite it
doi: 10.5281/zenodo.6515312
Written from nf-core/hicar's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.