runHiC

runHiC is an easy-to-use command-line tool for Hi-C data processing.

Since version 0.8.6, runHiC has supported data from all kinds of 3C-based experiments, including Hi-C, Micro-C, HiChIP/PLAC-Seq, and ChIA-PET. For experiments that do not use restriction enzymes for DNA fragmentation, you can set the enzyme name arbitrarily for your record. For example, for Micro-C, you can set it to MNase; for ChIA-PET, you can set it to sonication.

Since version 0.8.5, runHiC has changed the default aligner to chromap, which is comparable to bwa-mem in alignment accuracy, but runs over 10 times faster.

Since version 0.8.1, runHiC can be used directly on Arima HiC data by setting the enzyme name to Arima.

Since version 0.8.0, runHiC has changed its default data container/format from HDF5 to Pairs and Cooler.

Design Concepts

runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the ICE-corrected contact matrices. It currently contains 5 subcommands:

mapping	Map raw sequencing reads to a supplied genome. Support three read aligners: chromap, bwa and minimap2.
filtering	Perform read-level and fragment-level noise removing
binning	1.Generate contact matirx; 2. Perform ICE/matrix-balancing normalization
pileup	Perform the entire processing steps from mapping to binning
quality	Evaluate the quality of your Hi-C data

User Guide

• Install runHiC
  • Requirements
  • Install Requirements through Mamba
  • Install runHiC
• Quick Start
  • Data Preparation
  • Mapping
    • Usage
    • Create the Meta Data File
    • runHiC Command
  • Filtering
  • Binning
  • Pileup
• Parallel Computation
  • Example
• Experiment Quality Assessment
  • Statistic Table
  • Library-size Estimation
  • Read-pair Type Plotting
• Release Notes
  • Version 0.8.7 (01/19/2023)
  • Version 0.8.6 (05/24/2022)
  • Version 0.8.5 (08/15/2021)
  • Version 0.8.4-r1 (01/16/2021)
  • Version 0.8.4 (01/03/2021)
  • Version 0.8.3 (03/04/2019)
  • Version 0.8.2 (01/16/2019)
  • Version 0.8.1 (12/23/2018)
  • Version 0.8.0 (09/16/2018)
  • Version 0.7.0 (10/29/2017)
  • Version 0.6.6-r2 (05/04/2016)
  • Version 0.6.6-r1 (11/10/2015)
  • Version 0.6.6 (11/06/2015)
  • Version 0.6.5 (09/29/2015)
  • Version 0.6.4 (09/21/2015)
  • Version 0.6.3 (09/16/2015)
  • Version 0.6.2 (08/21/2015)
  • Version 0.6.1 (07/21/2015)
  • Version 0.6.0 (06/16/2015)

Citation

Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo. 10.5281/zenodo.55324