Skip to main content

A easy-to-use Hi-C processing software supporting distributed computation

Project description

https://zenodo.org/badge/doi/10.5281/zenodo.55324.svg

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

Since version 0.8.0, runHiC has changed its default data container/format from HDF5 to Pairs and Cooler, to comply with 4DN standards. (See Release Notes)

Design Concepts

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

mapping

Map raw pair-end sequencing data to a supplied genome. Support bwa and minimap2.

filtering

Perform read-level and fragment-level noise removing

binning

1.Generate contact matirx; 2. Perform ICE

pileup

Perform entire processing from mapping to binning

quality

Assess the quality of your Hi-C data

Usage

Open a terminal, type runHiC -h and runHiC <subcommand> -h for help information.

Citation

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

runHiC-0.8.0.post3.tar.gz (31.2 kB view hashes)

Uploaded Source

Built Distribution

runHiC-0.8.0.post3-py3-none-any.whl (20.1 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page