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.
@article{arxiv.2406.10610,
title = {String Partition for Building Long Burrows-Wheeler Transforms},
author = {Enno Adler and Stefan Böttcher and Rita Hartel},
journal= {arXiv preprint arXiv:2406.10610},
year = {2025}
}