cuttlefish.rst

Cuttlefish

Introduction ~~~~~~~~ Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from sequencing reads or reference sequences. It is highly scalable in terms of the size of the input data.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/cuttlefish
Home page: https://github.com/COMBINE-lab/cuttlefish

Versions

• 2.1.1

Commands ~~~~~~~ - cuttlefish

Module

You can load the modules by:

module load biocontainers
module load cuttlefish

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 cuttlefish on our clusters:

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

module --force purge
ml biocontainers cuttlefish