Computing the Original eBWT Faster, Simpler, and with Less Memory

Marinella Sciortino, Christina Boucher, Zsuzsanna Lipták, Massimiliano Rossi, Davide Cenzato

Risultato della ricerca: Conference contribution

5 Citazioni (Scopus)


Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings. However, since this introduction, it has been used more generally to describe any BWT of a collection of strings, and the fundamental property of the original definition (i.e., the independence from the input order) is frequently disregarded. In this paper, we propose a simple linear-time algorithm for the construction of the original eBWT, which does not require the preprocessing of Bannai et al. [CPM 2021]. As a byproduct, we obtain the first linear-time algorithm for computing the BWT of a single string that uses neither an end-of-string symbol nor Lyndon rotations. We combine our new eBWT construction with a variation of prefix-free parsing to allow for scalable construction of the eBWT. We evaluate our algorithm (pfpebwt) on sets of human chromosomes 19, Salmonella, and SARS-CoV2 genomes, and demonstrate that it is the fastest method for all collections, with a maximum speedup of 7.6 × on the second best method. The peak memory is at most 2 × larger than the second best method. Comparing with methods that are also, as our algorithm, able to report suffix array samples, we obtain a 57.1 × improvement in peak memory. The source code is publicly available at
Lingua originaleEnglish
Titolo della pubblicazione ospiteString Processing and Information Retrieval - 28th International Symposium, SPIRE 2021, Lille, France, October 4–6, 2021, Proceedings Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Numero di pagine14
Stato di pubblicazionePublished - 2021

Serie di pubblicazioni


All Science Journal Classification (ASJC) codes

  • ???subjectarea.asjc.2600.2614???
  • ???subjectarea.asjc.1700.1700???


Entra nei temi di ricerca di 'Computing the Original eBWT Faster, Simpler, and with Less Memory'. Insieme formano una fingerprint unica.

Cita questo