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Workflow type
Snakemake1
Submitter
Tom Brown1
Team
ERGA Assembly1
Creator
Tom Brown1
Topic annotations
Genome visualisation1
Operation annotations
Genome visualisation1
Genome assembly13
Sequencing quality control5
Scaffolding2
Contact map calculation1
Genome annotation1
k-mer counting1
Sequence profile generation1
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Maturity
Stable1
1
Workflow matching the given criteria:
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Operation annotations:
Genome visualisation1
Stable
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.
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 ...
