String Partition for Building Long Burrows-Wheeler Transforms

TL;DR

This paper introduces a partitioning strategy for long strings that improves the efficiency of constructing the Burrows-Wheeler transform by enabling faster processing and reduced memory usage, demonstrated with DNA sequences.

Contribution

The paper presents a novel string partitioning method using suffix array prefixes, enabling efficient BWT construction with a new implementation called partDNA for genomic data.

Findings

partDNA with IBB outperforms existing algorithms in speed and memory efficiency

Partitioning strategy is applicable to any alphabet and improves BWT construction for long strings

Experimental results on genome datasets validate the effectiveness of the approach

Abstract

Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby enabling the use of multi-string BWT construction algorithms to process these partitions fast. We provide an implementation, partDNA, for DNA sequences. Through comparison with state-of-the-art BWT construction algorithms, we show that partDNA with IBB offers a novel trade-off for construction time and memory usage for BWT construction on real genome datasets. Beyond this, the proposed partitioning strategy is applicable to strings of any alphabet.