Jellyfish
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Application data |
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| Created by | Guillaume Marçais, Carl Kingsford |
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| Created at | University of Maryland |
| Maintained? | Maybe |
| Programming language(s) | C++ |
| Licence | GPLv3 |
| Operating system(s) | Linux 64, Mac OS X |
| Contact: | gmarcais@umd.edu |
Summary: Fast, memory-efficient k-mer counting algorithm
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Description
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 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 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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