Workflows
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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
...
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 ...
ANNOTATO - Annotation workflow To Annotate Them Oll
ERGA Protein-coding gene annotation workflow.
Adapted from the work of Sagane Joye:
https://github.com/sdind/genome_annotation_workflow
Prerequisites
The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.
conda v 23.7.3
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