Difference between revisions of "R-index"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|r-index}} |{{#vardefine:url|https://github.com/alshai/r-index}} <!--CONFIGUR...") |
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_LIB - library directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_INC - include directory |
<!--Configuration--> | <!--Configuration--> | ||
Latest revision as of 21:24, 6 December 2019
Description
The r-index is the first full-text index of size O(r), r being the number of BWT runs of the input text (of size n), supporting fast (almost optimal) locate of pattern occurrences. The r-index employs a novel suffix array sampling of size 2r; in classical FM-indexes, this sampling would result in a locate time of Omega(n/r) per occurrence. The r-index, on the other hand, reduces this time to O(log(n/r)).
Environment Modules
Run module spider r-index to find out what environment modules are available for this application.
System Variables
- HPC_R-INDEX_DIR - installation directory
- HPC_R-INDEX_LIB - library directory
- HPC_R-INDEX_INC - include directory
Citation
If you publish research that uses r-index you have to cite it as follows:
WRITE_CITATION_HERE