BWT construction and search at the terabase scale

Abstract

Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction is resource intensive and hard to be parallelized, and many methods for querying large full-text indices only report exact matches or their simple extensions. These limitations have hampered the biological applications of full-text indices. Results: We developed ropebwt3 for efficient BWT construction and query. Ropebwt3 could index 100 assembled human genomes in 21 hours and index 7.3 terabases of commonly studied bacterial assemblies in 26 days. This was achieved using 82 gigabytes of memory at the peak without working disk space. Ropebwt3 can find maximal exact matches and inexact alignments under affine-gap penalties, and can retrieve all distinct local haplotypes matching a query sequence. It demonstrates the feasibility of full-text indexing at the terabase scale. Availability and implementation: https://github.com/lh3/ropebwt3