runHiC
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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 <https://github.com/haowenz/chromap>
,
which is comparable to bwa-mem <https://github.com/lh3/bwa>
in alignment accuracy, but runs over 10 times faster.
Since version 0.8.1, runHiC can be used directly on Arima HiC <https://arimagenomics.com>
_ 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 <https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md>
and
Cooler <https://github.com/mirnylab/cooler>
.
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 | +------------+-------------------------------------------------------------------------------------------------------------------+
Detailed Documentation <http://xiaotaowang.github.io/HiC_pipeline/>
_
Installation <http://xiaotaowang.github.io/HiC_pipeline/install.html>
_Quick Start <http://xiaotaowang.github.io/HiC_pipeline/quickstart.html>
_Data Quality <http://xiaotaowang.github.io/HiC_pipeline/quality.html>
_Parallel Computation <http://xiaotaowang.github.io/HiC_pipeline/parallel.html>
_Code Repository <https://github.com/XiaoTaoWang/HiC_pipeline/>
_ (At GitHub, Track the package issue)PyPI <https://pypi.python.org/pypi/runHiC>
_ (Download and Installation)Open a terminal, type runHiC -h
or runHiC <subcommand> -h
for help information.
Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo.
10.5281/zenodo.55324 <http://dx.doi.org/10.5281/zenodo.55324>
_