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1 SAIS-OPT: On the Characterization and Optimization of the SA-IS Algorithm for Suffix Array Construction
BibTeX
@MISC{Timoshevskaya_1sais-opt:,
author = {Nataliya Timoshevskaya and Wu-chun Feng},
title = {1 SAIS-OPT: On the Characterization and Optimization of the SA-IS Algorithm for Suffix Array Construction},
year = {}
}
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Abstract
Abstract—The suffix array and Burrows-Wheeler Transform are critical index structures in next generation sequence analysis. The construction of such index structures for mammalian-sized genomes can take thousands of seconds (i.e. tens of minutes). Its construction is complicated by computational overheads that coming from irregular or complex memory-access patterns. This paper rigorously characterizes the execution profile of the SA-IS algorithm in order to guide its optimization. The resulting optimized SA-IS, which we refer to as sais-opt, outperforms previous implementations of SA-IS as well as “best in practice” algorithms, when applied to large DNA strings. Keywords—suffix array; Burrows-Wheeler Transform; irregular memory access
Keyphrases
sa-is algorithm suffix array construction burrows-wheeler transform mammalian-sized genome execution profile practice algorithm previous implementation large dna string optimized sa-is keywords suffix array critical index structure suffix array complex memory-access pattern index structure next generation sequence analysis irregular memory access computational overhead
