View source for R-index

[[Category:Software]][[Category:Phylogenetics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|r-index}}
|{{#vardefine:url|https://github.com/alshai/r-index}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
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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)).

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{{#if: {{#var: testing}}|==Performance==

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{{#if: {{#var: faq}}|==FAQ==
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