Hi-C processing pipeline in snakemake.
This pipeline takes cares of (optional) download of raw sequencing reads from sequencing read archives, alignment using bwa
, .pairs
or .pairsam
file generation and pair filtering using pairtools
, and finally contact matrix generation using cooler
.
- Clone the repo.
$ git clone https://github.com/dohlee/snakemake-hic-processing.git
$ cd snakemake-hic-processing
-
Modify the configuration
config.yaml
andmanifest.csv
as you want. -
Create conda environment for this pipeline and run it. Consider using
mamba
if downloading packages takes long time.
$ conda env create -f environment.yaml
This pipeline is mostly similar to the official Hi-C Processing Pipeline in 4D nucleome project: https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline. See also the official github repository https://github.com/4dn-dcic/docker-4dn-hic/tree/v43.