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HiCExplorer

HiCExplorer is a suite of command-line tools to process, normalize, analyze and visualize Hi-C, Micro-C and capture Hi-C (cHi-C) data. This is version 4.

What is new in version 4

  • Faster, much less memory. On a real single-chromosome Hi-C matrix (24,926 bins, 61.8M nonzero pixels), the tools of version 4 measured 5 to 70 times faster than HiCExplorer 3.7.6, single-threaded, at 3 to 9 times less peak memory. Most tools also run multithreaded. See Benchmarks for the numbers.
  • The same results. Every tool is checked against the output of HiCExplorer 3.7.6 on real and synthetic data. Command lines, file formats and outputs stay compatible, and known differences are listed on the page of the tool.
  • CHiCAGO scoring. The chicChicago* tools score capture Hi-C interactions with the CHiCAGO method from cool, h5 or .hic matrices, and plot them as viewpoints, arcs and genome tracks. See the CHiCAGO tutorial.
  • New analysis tools. hicDifferentialAnalysis (replicate-aware differential TADs, loops and compartments) and hicDetectStripes.
  • One package. conda install hicexplorer installs the tools together with the Python API. Existing scripts that call the commands or import hicexplorer keep working.

At a glance

# build a Hi-C matrix from two independently mapped SAM/BAM files
hicBuildMatrix --samFiles mate_R1.bam mate_R2.bam \
  --binSize 10000 --restrictionSequence GATC --danglingSequence GATC \
  --restrictionCutFile cut_sites.bed --outBam hic.bam \
  -o hic_matrix.cool --QCfolder ./hicQC

# correct the matrix (Knight-Ruiz, the default)
hicCorrectMatrix correct -m hic_matrix.cool -o hic_corrected.cool

# call TADs
hicFindTADs -m hic_corrected.cool --outPrefix hic_corrected

Where to go next

  • Installation: installing with conda, pip or from source.
  • Usage: the general command-line conventions shared by all tools.
  • Tools: the full list of tools, grouped by task, each with its own CLI reference.
  • File formats: the native h5/cool matrix format and the capture Hi-C HDF containers.
  • Example usage: a worked pre-processing-to-visualization walkthrough.
  • Benchmarks: runtime and memory compared with HiCExplorer 3.7.6.
  • News: the release history.
  • Citation: how to cite HiCExplorer.
  • Support: where to get help.