sourmash
Link to section 'Introduction' of 'sourmash' Introduction
Sourmash is a tool for quickly search, compare, and analyze genomic and metagenomic data sets.
For more information, please check its website: https://biocontainers.pro/tools/sourmash and its home page on Github.
Link to section 'Versions' of 'sourmash' Versions
- 4.3.0
- 4.5.0
Link to section 'Commands' of 'sourmash' Commands
- sourmash
Link to section 'Module' of 'sourmash' Module
You can load the modules by:
module load biocontainers
module load sourmash
Link to section 'Example job' of 'sourmash' 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 Sourmash on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sourmash
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers sourmash
sourmash sketch dna -p k=31 *.fna.gz
sourmash compare *.sig -o cmp.dist
sourmash plot cmp.dist --labels