Workflow Type: Snakemake

HiC contact map generation

Snakemake pipeline for the generation of .pretext and .mcool files for visualisation of HiC contact maps with the softwares PretextView and HiGlass, respectively.


This pipeine has been tested using Snakemake v7.32.4 and requires conda for installation of required tools. To run the pipline use the command:

snakemake --use-conda

There are provided a set of configuration and running scripts for exectution on a slurm queueing system. After configuring the cluster.json file run:


Before starting

You need to create a temporary folder and specify the path in the config.yaml file. This should be able to hold the temporary files created when sorting the .pairsam file (100s of GB or even many TBs)

The path to the genome assemly must be given in the config.yaml.

The HiC reads should be paired and named as follows: Library_1.fastq.gz Library_2.fastq.gz. The pipeline can accept any number of paired HiC read files, but the naming must be consistent. The folder containing these files must be provided in the config.yaml.

Version History

Version 2 (latest) Created 29th Apr 2024 at 13:22 by Tom Brown

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Version 1 (earliest) Created 14th Mar 2024 at 09:50 by Tom Brown

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Brown, T. (2024). HiC contact map generation. WorkflowHub.

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Created: 14th Mar 2024 at 09:50

Last updated: 14th Mar 2024 at 09:52

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