Unicycler is an assembly pipeline for bacterial genomes.

• Version: 0.5.0
• Added: February, 2019
• Updated: June, 2023
• Link: https://github.com/rrwick/Unicycler

See versions which are available:

$ module avail unicycler

Load one version into your environment and run it:

$ module load unicycler/0.5.0
$ unicycler

#!/usr/bin/env bash
#SBATCH -p batch
#SBATCH -n 4
#SBATCH -J unicycler

module load unicycler/0.5.0

readonly DATADIR=~/sample_data
readonly OUTDIR=/var/scratch/2019-02-15-aorth-unicycler

# create output directory on compute node
mkdir -p ${OUTDIR}

# run unicycler with the number of threads allocated by SLURM
unicycler -t ${SLURM_NTASKS} -1 ${DATADIR}/short_reads_1.fastq.gz -2 ${DATADIR}/short_reads_2.fastq.gz -o ${OUTDIR}

echo
echo "Remember to check (and clean!) output directory on ${SLURM_JOB_NODELIST}:"
echo
echo "  ${OUTDIR}"

By default Unicycler will use four CPU threads. Please make sure to set this parameter properly according to the SLURM job request.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/rrwick/Unicycler/archive/refs/tags/v0.5.0.tar.gz
$ tar xf v0.5.0.tar.gz
$ cd Unicycler-0.5.0
$ module load python/3.8
$ sudo mkdir -p /export/apps/unicycler/0.5.0
$ sudo chown aorth /export/apps/unicycler/0.5.0
$ python3.8 setup.py install --prefix=/export/apps/unicycler/0.5.0
$ sudo chown -R root:root /export/apps/unicycler/0.5.0