HybPiper

HybPiper has been centrally installed on the cluster using a wrapper script, this slightly changes how it operates. loading the module loads all of the dependencies

module load hybpiper/1.3.1

Usage Example

This is a basic template of how to run reads first in a bash script on KewHPC

#!/bin/bash
#SBATCH -J hybpiper_example
#SBATCH -e /data/users_area/myuser/errout/hybpiper_%A.err
#SBATCH -o /data/users_area/myuser/errout/hybpiper_%A.out
#SBATCH -c 8 
#SBATCH -p all

module load hybpiper/1.3.1

name="miseq_run_GTCATA_L001"
hybpiper reads_first    --cpu 8 \
                        -b /data/users_area/myuser/baitfile.fasta \
                        -r /data/users_area/myuser/$name\_R*.fastq \
                        --unpaired /data/users_area/myuser/$name.fastq \
                        --prefix seqdata \
                        --cov_cutoff 4 
hybpiper cleanup $name