Direct construction of sparse suffix arrays with Libsais
We introduce an efficient method for the construction of sparse suffix arrays for large datasets. Central to this approach is the introduction of a simple text transformation, which then serves as input to Libsais. This method reduces the length of both the input text and the resulting suffix array by a factor of k, which improves execution time and memory usage significantly.
Authors
- Peter Dawyndt (ORCID: https://orcid.org/0000-0002-1623-9070)
- Bart Mesuere (ORCID: https://orcid.org/0000-0003-0610-3441)
- Tibo Vande Moortele (ORCID: https://orcid.org/0000-0002-7813-934X)
- Pieter Verschaffelt (ORCID: https://orcid.org/0000-0002-6675-1048)
- Simon Van de Vyver (ORCID: https://orcid.org/0009-0009-7810-2174)
Institutions
- HOGENT University of Applied Sciences and Arts (BE)
- Ghent University Hospital (BE)
- Ghent University (BE)
- VIB-UGent Center for Medical Biotechnology (BE)
Publication Details
- Journal
- BMC Bioinformatics
- Published
- 2025-10-17
- DOI
- https://doi.org/10.1186/s12859-025-06277-z
- Primary Topic
- Algorithms and Data Compression
- Type
- article
- Field-Weighted Citation Impact
- 0.00