merqury.rst

Merqury

Introduction ~~~~~~~~ Merqury is a tool to evaluate genome assemblies with k-mers and more.

For more information, please check:
Docker hub: https://hub.docker.com/r/dovetailg/merqury
Home page: https://github.com/marbl/merqury

Versions

• 1.3

Commands ~~~~~~~ - merqury.sh

Module

You can load the modules by:

module load biocontainers
module load merqury

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 merqury on our clusters:

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

module --force purge
ml biocontainers merqury

merqury.sh F1.k18.meryl col0.hapmer.meryl cvi0.hapmer.meryl \
    athal_COL.fasta athal_CVI.fasta test