Genomescope2

Introduction

Genomescope2: Reference-free profiling of polyploid genomes.

For more information, please check its website: https://biocontainers.pro/tools/genomescope2 and its home page on Github.

Versions

  • 2.0

Commands

  • genomescope2

Module

You can load the modules by:

module load biocontainers
module load genomescope2

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 Genomescope2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genomescope2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers genomescope2

wget https://raw.githubusercontent.com/schatzlab/genomescope/master/analysis/real_data/ara_F1_21.hist

genomescope2 -i ara_F1_21.hist -o output -k 21