Nanolyse

Introduction

Nanolyse is a tool to remove reads mapping to the lambda phage genome from a fastq file.

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

Versions

• 1.2.0

Commands

• NanoLyse

Module

You can load the modules by:

module load biocontainers
module load nanolyse

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 Nanolyse on our clusters:

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

module --force purge
ml biocontainers nanolyse

gunzip -c reads.fastq.gz |  NanoLyse |  gzip > reads_without_lambda.fastq.gz