jellyfish

Jellyfish is a tool for memory-efficient, fast k-mer counting in DNA files. It has the capacity to utilize compare and swap cpu instruction sets to improve parallelism. The output will depend upon which subcommand used, but by default it will report k-mers to mer_counts.jf.

For additional information and examples see the documentation

Execution:

ml biocontainers jellyfish
jellyfish count -m 21 -s 100M -t 10 -C input.fasta

Parallel Capabilities: Single core default, Multithreading options supported.