URL: http://www.genome.umd.edu/jellyfish.html
Proper Citation: Jellyfish (RRID:SCR_005491)
Description: A software 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.
Abbreviations: Jellyfish
Synonyms: Jellyfish mer counter
Resource Type: software resource
Defining Citation: PMID:21217122, DOI:10.1093/bioinformatics/btr011
Keywords: c++, bio.tools
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