plotsr.rst

Plotsr

Introduction ~~~~~~~~ Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.

For more information, please check:
Home page: https://github.com/schneebergerlab/plotsr

Versions

• 0.5.4

Commands ~~~~~~~ - plotsr

Module

You can load the modules by:

module load biocontainers
module load plotsr

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 plotsr on our clusters:

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

module --force purge
ml biocontainers plotsr

plotsr syri.out refgenome qrygenome -H 8 -W 5