Jellyfish counts k-mers in fasta or fastq files (and sam/bam/cram starting at version 2.2.7). k-mer counts are saved in a binary format that can be queried or dumped to text based format.

References:

• G. Marcais and C. Kingsford. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 2011, 27:764-770. PubMed |  PMC |  Journal

• GitHub
• Manual [pdf]
• Home page

• Module Name: jellyfish (see the modules page for more information)
• jellyfish is a multithreaded application. Please match the number of threads to the number of allocated CPUs
• Example files can be found in $JELLYFISH_TEST_DATA
• Some versions of jellyfish have a but when counting 7- or 8-mers.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=6 --mem=10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load jellyfish
[user@cn3144 ~]$ cp -L $JELLYFISH_TEST_DATA/* .
[user@cn3144 ~]$ ls -lh
total 445M
-rw-r--r-- 1 user group 387M Feb 24 13:59 ENCFF001NGB.bam
-rw-r--r-- 1 user group  56M Feb 24 13:59 ERR458495.fastq.gz

[user@cn3144 ~]$ # count 16-mers in fastq file (S. cerevisiae RNA-Seq data)
[user@cn3144 ~]$ # jellyfish does not natively read compressed data - uncompress on the fly
[user@cn3144 ~]$ jellyfish count -t $SLURM_CPUS_PER_TASK \
                        -m 16 -s 10M -C -o 16mer.jf <(zcat ERR458495.fastq.gz)
[user@cn3144 ~]$ ls -lh 16mer.jf
-rw-r--r-- 1 user group 51M Feb 26 07:54 16mer.jf
[user@cn3144 ~]$ jellyfish stats 16mer.jf
Unique:    3319471
Distinct:  6625582
Total:     38369851
Max_count: 2284

[user@cn3144 ~]$ jellyfish dump -L 2 -o 16mer.fa 16mer.jf
[user@cn3144 ~]$ head 16mer.fa
>259
AAAAAAAAAAAAAAAA
>3
CAATTTAGCCTTTCGC
>2
CTCATCCATGTGAAAA
>2
AAGTCAGGCACAAATC
>2
CTTCATTTTGCCACCA

[user@cn3144 ~]$ jellyfish query 16mer.jf AGCCAATTTGACTTCA
AGCCAATTTGACTTCA 45
[user@cn3144 ~]$ jellyfish histo -t $SLURM_CPUS_PER_TASK 16mer.jf > hist
[user@cn3144 ~]$ head -5 hist
1 3319471
2 1114139
3 594139
4 359875
5 238815

[user@cn3144 ~]$ # count 16mers in alinged mouse data in bam format
[user@cn3144 ~]$ jellyfish count -t $SLURM_CPUS_PER_TASK -m 16 -s 10M -C \
                        -o mouse_16mers.jf --sam ENCFF001NGB.bam

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. jellyfish.sh), which uses the input file 'jellyfish.in'. For example:

#!/bin/bash
module load jellyfish/2.2.7 || exit 1
jellyfish count -t $SLURM_CPUS_PER_TASK -m 16 -s 10M -C \
    -o mouse_16mers.jf --sam ENCFF001NGB.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=10g jellyfish.sh

Create a swarmfile (e.g. jellyfish.swarm). For example:

jellyfish count -t $SLURM_CPUS_PER_TASK -m 12 -s 10M -o sample1_12.jf --sam sample1.bam
jellyfish count -t $SLURM_CPUS_PER_TASK -m 12 -s 10M -o sample2_12.jf --sam sample2.bam
jellyfish count -t $SLURM_CPUS_PER_TASK -m 12 -s 10M -o sample3_12.jf --sam sample3.bam

Submit this job using the swarm command.

swarm -f jellyfish.swarm -g 10 -t 4 --module jellyfish/2.2.7