View on GitHub

snHiC

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

update

New analyses implemented: Tad calling also by GENOVA, Loop detection also by Mustache, stripes detection by STRIPENN, differential contacts caling by SELFISH.
Yaml environment updated
Providing of a bash script for the installation, fixing and configuration of packages/softwares not included in the yaml file
Reorganization of the manual in a GitHub-Wiki
Implementation of the becnhmarking in the snakemake pipeline
Re-formatting and update of the config file
Providing of testa fastq files as well as resulting outputs
Pipeline has been published on Bioinformatics Advances (DOI: 10.1093/bioadv/vbad080)

Implemented the use of bwa-mem2 instead of bwa in order to reduce the time required for the mapping. It follows that both snakemake file and yaml-formatted environment files have been updated.
Added a folder containing the dcHiC logs in the compartments folder.