Difference between revisions of "Jellyfish"
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"jellyfish dump" command. | "jellyfish dump" command. | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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Revision as of 13:31, 13 June 2022
Description
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.
System Variables
- HPC_JELLYFISH_DIR - installation directory
- HPC_JELLYFISH_BIN - executable directory
- HPC_JELLYFISH_BIN - includes directory