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.
This package is built using SPACK and optimized for AVX, AVX2 and AVX512 CPUs. To use the optimized version, you need to add source /etc/profile.d/zlmod.sh to your submit script before loading any modules. By default, the AVX2 optimized version (head node is Haswell CPU) is in your path. The AVX2 optimized version will run on Skylake (enge, im2080, chem, health) and Cascade Lake (hawkcpu, hawkmem, hawkgpu, infolab) CPUs but not on Ivybridge (debug) CPUs.
| Version | module name |
|---|---|
| 2.2.7 | jellyfish/2.2.7 |
For more information visit http://www.cbcb.umd.edu/software/jellyfish/