Purge dups

This snakemake pipeline is designed to be run using as input a contig-level genome and pacbio reads. This pipeline has been tested with snakemake v7.32.4. Raw long-read sequencing files and the input contig genome assembly must be given in the config.yaml file. To execute the workflow run:

snakemake --use-conda --cores N

Or configure the cluster.json and run using the ./run_cluster command

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 ...