On the Optimisation of the GSACA Suffix Array Construction Algorithm
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.
Keywords
Cite
@article{arxiv.2206.12222,
title = {On the Optimisation of the GSACA Suffix Array Construction Algorithm},
author = {Jannik Olbrich and Enno Ohlebusch and Thomas Büchler},
journal= {arXiv preprint arXiv:2206.12222},
year = {2022}
}