Unicycler

Introduction

Unicycler is an assembly pipeline for bacterial genomes.

For more information, please check its website: https://biocontainers.pro/tools/unicycler and its home page on Github.

Versions

0.5.0

Commands

unicycler

Module

You can load the modules by:

module load biocontainers
module load unicycler

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 Unicycler on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=unicycler
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers unicycler

unicycler -t 12 -1 SRR11234553_1.fastq  -2 SRR11234553_2.fastq -o shortout

unicycler -t 12  -l SRR3982487.fastq  -o longout