KeBaB: $k$-mer based breaking for finding long MEMs
Data Structures and Algorithms
2025-06-10 v3
Abstract
Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can often ignore much of its input. In this paper we show that a fast and space efficient -mer filtration step using a Bloom filter speeds up MEM-finders such as ropebwt3 even further by letting them ignore even more. We also show experimentally that our approach can accelerate metagenomic classification without significantly hurting accuracy.
Cite
@article{arxiv.2502.20338,
title = {KeBaB: $k$-mer based breaking for finding long MEMs},
author = {Nathaniel K. Brown and Lore Depuydt and Mohsen Zakeri and Anas Alhadi and Nour Allam and Dove Begleiter and Nithin Bharathi Kabilan Karpagavalli and Suchith Sridhar Khajjayam and Hamza Wahed and Travis Gagie and Ben Langmead},
journal= {arXiv preprint arXiv:2502.20338},
year = {2025}
}