HiC contact map generation
Download RO-CrateHiC 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.
Prerequisites
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:
./run_cluster
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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Created: 14th Mar 2024 at 09:50
Last updated: 14th Mar 2024 at 09:52
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A collection of workflows and pipelines developed as part of the ERGA consortium
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Collection of workflows designed to assembled a set of PacBio HiFi and Illumina HiC reads into a chromosome-scale de-novo assembly.
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