Software: k-mer Jellyfish
Description
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.
Available Versions
| Unspecified: | 2.3.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/kmer-jellyfish and its home page: http://www.genome.umd.edu/jellyfish.html.
Commands
- jellyfish
Module
You can load the modules by:
module load biocontainers
module load kmer-jellyfish
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run Jellyfish on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=kmer-jellyfish
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers kmer-jellyfish
jellyfish count -m 16 -s 100M -t 12 \
-o mer_counts -c 7 input.fastq