Installation

First, make sure you have the third party dependencies:

• samtools
• minimap2
• bowtie2

You can then install hicstuff latest stable version using pip:

pip3 install --user hicstuff

Or the latest development (unstable) version using:

pip3 install -e git+https://github.com/koszullab/hicstuff.git@master#egg=hicstuff

Quickstart

The fastest way to generate Hi-C matrices is to use the hicstuff pipeline command:

hicstuff pipeline -g bt2_index for.fq rev.fq

However, you most likely want to have a look at the command line help to select appropriate options, such as the enzyme used in the experiment. The help can be displayed using:

hicstuff pipeline --help

Matrices generated in the default coordinate format can then be visualised using the view command, modified using the rebin and convert commands, or used as input for other softwares.