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SOPanG: online text searching over a pan-genome

A. Cislak, S. Grabowski, J. Holub,

. 2018 ; 34 (24) : 4290-4292. [pub] 20181215

Language English Country Great Britain

Document type Journal Article, Research Support, Non-U.S. Gov't

Persistent link   https://www.medvik.cz/link/bmc19045399

Motivation: The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far. Results: We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400 MB/s, more than an order of magnitude higher than of other software. Availability and implementation: SOPanG is available for free from: https://github.com/MrAlexSee/sopang. Supplementary information: Supplementary data are available at Bioinformatics online.

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