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.
Jellyfish can count k-mers quickly 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 containing DNA sequences. It outputs its k-mer counts in an binary
format, which can be translated into a human-readable text format using
the "jellyfish dump" command. See the documentation below for more
details.
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