Jellyfish and comb jellies are gelatinous animals that drift through the ocean's water column around the world. They are both beautiful—the jellyfish with their pulsating bells and long, trailing tentacles, and the comb jellies with their paddling combs generating rainbow-like colors.

Yet though they look similar in some ways, jellyfish and comb jellies are not very close relatives being in different phyla—Cnidaria and Ctenophora, respectively and have very different life histories. Both groups are ancient animals, having roamed the seas for at least 500 million years. And, in the modern age, they are having similar effects on ecosystems. As seawater...

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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. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.

JELLYFISH is a command-line program that reads FASTA and multi-FASTA files jellyfish DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using...

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