cuttlefish
Link to section 'Introduction' of '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.
BioContainers: https://biocontainers.pro/tools/cuttlefish
Home page: https://github.com/COMBINE-lab/cuttlefish
Link to section 'Versions' of 'cuttlefish' Versions
- 2.1.1
Link to section 'Commands' of 'cuttlefish' Commands
- cuttlefish
Link to section 'Module' of 'cuttlefish' Module
You can load the modules by:
module load biocontainers
module load cuttlefish
Link to section 'Example job' of '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