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Jellyfish

Version: 
2.3.0 (G100)

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 documentation for details. 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

Target user: 
all
Support level: 
medium
Help and documentation: 

You can find documentation on the system, with the command

module help vcftools

To see a list of alla available tools, run

 man vcftools

Or visit the Documentation page: https://vcftools.github.io/man_latest.html

CINECA consultants can be reached through the address: superc@cineca.it

Deadline: 
01/02/2024