Space Efficient Suffix Array Construction using Induced Sorting LMS Substrings

Yelchuri, Rajesh; Rao.N, Nagamalleswara

doi:10.5121/ijist.2013.3402

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2014

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“…For example, SAR-IS [15] and SACA-K [16] reduce space consumption, while bwa-is and sais-lite significantly improve both, when compared to the original implementation of SA-IS [9]. Our work addresses the memory-bounded character of SA-IS algorithm.…”

Section: Related Workmentioning

confidence: 99%

SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction

Timoshevskaya

Feng

2014

2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

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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.

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Section: Related Workmentioning

confidence: 99%