HiC scaffolding pipeline

Snakemake pipeline for scaffolding of a genome using HiC reads using yahs.

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 --cores N

where N is number of cores to use. 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 ...