Jellyfish¶

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 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.

Environment Modules¶

Run module spider jellyfish to find out what environment modules are available for this application.

Environment Variables¶

HPC_JELLYFISH_DIR - installation directory
HPC_JELLYFISH_BIN - executable directory
HPC_JELLYFISH_LIB - libraries directory
HPC_JELLYFISH_INC - includes directory

Categories¶

biology, ngs