blobtools.rst

BlobTools

Introduction ~~~~~~~ BlobTools is a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.

Detailed usage can be found here: https://github.com/DRL/blobtools

Versions

• 1.1.1

Commands ~~~~~~ - blobtools

Module

You can load the modules by:

module load biocontainers
module load blobtools/1.1.1

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 blobtools on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=blobtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers blobtools/1.1.1

blobtools create -i example/assembly.fna -b example/mapping_1.sorted.bam -t example/blast.out -o test && \
blobtools view -i test.blobDB.json && \
blobtools plot -i test.blobDB.json