Software: Cuttlefish
Description
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.
Available Versions
Unspecified: | 2.1.1 |
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BioContainers: https://biocontainers.pro/tools/cuttlefish
Home page: https://github.com/COMBINE-lab/cuttlefish
Commands
- cuttlefish
Module
You can load the modules by:
module load biocontainers
module load cuttlefish
Example job
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