Parallel computation of the Burrows Wheeler Transform in compact space

Document Type

Article

Publication Date

9-23-2019

Department

Department of Computer Science

Abstract

The Burrows-Wheeler Transform (BWT) has become since its introduction a key tool for representing large text collections in compressed space while supporting indexed searching: on a text of length n over an alphabet of size Οƒ, it requires O(𝑛 1g Οƒ) bits of space, instead of the O(𝑛 1g 𝑛) bits required by classical indexes. A challenge for its adoption is to build it within O(𝑛 1g Οƒ) bits as well. There are some sequential algorithms building it within this space, but no such a parallel algorithm. In this paper we present a PRAM CREW algorithm to build the BWT using O(𝑛 1√1g 𝑛) work, O(1g3 𝑛/1g Οƒ) depth, and O(𝑛 1g Οƒ) bits.

Publication Title

Theoretical Computer Science

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