Difference between revisions of "Jellyfish"
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Moskalenko (talk | contribs) (Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|jellyfish}} |{{#vardefine:url|http://www.genome.umd.edu/jellyfish.html}} <!--CONFIGURATION: OPTIONAL (...") |
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| − | [[Category:Software]] | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|jellyfish}} | |{{#vardefine:app|jellyfish}} | ||
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"jellyfish dump" command. | "jellyfish dump" command. | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{# | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - includes directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 19:27, 12 August 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