Kmer Counting Commands

 # counting
 jellyfish count -m 31 -s 200M -t 10 -C shortreads.fasta
 jellyfish count -m 31 -s 4G --bf-size 100G -t 10 -C shortreads.fasta
 # histogram
 jellyfish histo mer_counts.jf
 # query count of a k-mer
 jellyfish query mer_counts.jf AATGATG
 # text dump
 jellyfish dump mer_counts.jf > text-count.fa

References

Manual

http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf http://www.cbcb.umd.edu/software/jellyfish/

Github

https://github.com/gmarcais/Jellyfish

Paper

https://academic.oup.com/bioinformatics/article/27/6/764/234905