HPC Module: Jellyfish
Synopsis
Adds JellyFish software to your environment.
| About This Software | |
|---|---|
| Official Site | https://github.com/gmarcais/Jellyfish |
| Tags |
Installed Versions
| Version | Install Date | Default? |
|---|---|---|
| 2.2.6 | 2016-12-06 |
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 a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the UserGuide provided on Jellyfish's home page for more details.
Citation(s)
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:10.1093/bioinformatics/btr011
Category
| Library | Programming | Software | SysAdmin |
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