N50

Introduction

N50 is a command line tool to calculate assembly metrices.

For more information, please check:

BioContainers: https://biocontainers.pro/tools/n50

Home page: https://github.com/quadram-institute-bioscience/seqfu/wiki/n50

Versions

• 1.5.6

Commands

• n50

Module

You can load the modules by:

module load biocontainers
module load n50

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 n50 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=n50
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers n50