jellyfish 1.1.2-1 (amd64 binary) in ubuntu quantal
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.
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If you use JELLYFISH in your research, please cite:
Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for
efficient parallel counting of occurrences of k-mers. Bioinformatics
(2011) 27(6): 764-770 (first published online January 7, 2011)
doi:10.
Details
- Package version:
- 1.1.2-1
- Status:
- Superseded
- Component:
- universe
- Priority:
- Optional
Downloadable files
- jellyfish_1.1.2-1_amd64.deb (369.5 KiB)
Package relationships
- Depends on: