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arXiv · 2206.12222

On the Optimisation of the GSACA Suffix Array Construction Algorithm

Jannik Olbrich·Enno Ohlebusch·Thomas Büchler
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Abstract

The suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known non-recursive linear-time suffix array construction algorithm (SACA). Despite its interesting theoretical properties, there has been little effort in improving the algorithm's subpar real-world performance. There is a super-linear algorithm DSH which relies on the same sorting principle and is faster than DivSufSort, the fastest SACA for over a decade. This paper is concerned with analysing the sorting principle used in GSACA and DSH and exploiting its properties in order to give an optimised linear-time algorithm. Our resulting algorithm is not only significantly faster than GSACA but also outperforms DivSufSort and DSH.

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Jannik Olbrich, Enno Ohlebusch, Thomas Büchler. 2022-06-24. On the Optimisation of the GSACA Suffix Array Construction Algorithm. https://arxiv.org/abs/2206.12222

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