Computing the multi-string BWT and LCP array in external memory

• Published in: Theoretical computer science Vol. 862; pp. 42 - 58
• Main Authors: Bonizzoni, Paola, Della Vedova, Gianluca, Pirola, Yuri, Previtali, Marco, Rizzi, Raffaella
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 16.03.2021
• Subjects: Burrows–Wheeler transform; External-memory algorithms; Longest common prefix array; Burrows–Wheeler transform; Longest common prefix array; External-memory algorithms
• ISSN: 0304-3975; 1879-2294; 1879-2294
• DOI: 10.1016/j.tcs.2020.11.041

Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multi-string generalization of the Burrows–Wheeler Transform (BWT): large requirements of in-memory approaches have stimulated recent developments on external memory algorithms. The related problem of computing the Longest Common Prefix (LCP) array of a set of strings is instrumental to compute the suffix-prefix overlaps among strings, which is an essential step for many genome assembly algorithms. In a previous paper, we presented an in-memory divide-and-conquer method for building the BWT and LCP where we merge partial BWTs with a forward approach to sort suffixes. In this paper, we propose an alternative backward strategy to develop an external memory method to simultaneously build the BWT and the LCP array on a collection of m strings of different lengths. The algorithm over a set of strings having constant length k has O(mkl) time and I/O volume, using O(k+m) main memory, where l is the maximum value in the LCP array.