Purdue University

Commands

• nanopolish

Module

You can load the modules by:

module load biocontainers
module load nanopolish

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Nanopolish on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=nanopolish
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers nanopolish

nanopolish index -d fast5_files/ reads.fasta

nanopolish variants --consensus \
    -o polished.vcf -w "tig00000001:200000-202000" \
     -r reads.fasta -b reads.sorted.bam  -g draft.fa