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