Demonstration of easy mammalian optimization for whole animal genome sequencing pipelines
(Importantly this repository acronym/title has nothing to do with JABBA)
This repo contains the steps required to setup a snakemake environment in order to process FASTQs to GVCFs and ultimately a joint genotyped VCF, all using a Singularity container.
Please see the main repository WAGS.
Download the equine container
Due to the size of the Equine genome and associated indices included in the container (and depending on your internet speed) this should take ~2 minutes.
wget https://s3.msi.umn.edu/wags/demo/horse_wags.sif
Download the data
wget https://s3.msi.umn.edu/wags/samples.tar.gz
tar -xzvf samples.tar.gz
Clone the WAGS repo
git clone https://github.com/jonahcullen/wags.git