Minipolish

Introduction

Minipolish is a tool for Racon polishing of miniasm assemblies.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/minipolish

Home page: https://github.com/rrwick/Minipolish

Versions

• 0.1.3

Commands

• minipolish

Example job

Warning

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 minipolish on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=minipolish
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load minipolish/XXXX ### you can run *module avail minipolish* to check all available versions

minipolish -t 8 long_reads.fastq.gz assembly.gfa > polished.gfa