2026-08-28T20:53:43Z https://drops.dagstuhl.de/oai

oai:drops-oai.dagstuhl.de:27531 2026-08-27T06:04:08Z ddc:004 open_access

Finimap: Fast and Accurate Single-Species Bacterial Pseudoalignment with Finimizers Alanko, Jarno N. Biagi, Elena Puglisi, Simon J. Pseudoalignment sequence alignment approximate string matching string processing k-mer data structures data compression In recent years, pseudoalignment as a means for mapping reads to databases of reference genomes has become a widely-used method in studies of bacterial pathogenesis. A popular pseudoalignment criterion is thresholded union, in which a read is said to pseudoalign to a reference if the reference contains more than a percentage t of the read’s k-mers. Several pseudoalignment indexing tools that implement this and other pseudoalignment criteria are now available, including Bifrost, Themisto, and Fulgor. In this paper, we describe a scheme for single-species bacterial pseudoalignment that, instead of k-mers, uses shortest unique finimizers (Alanko et al., IEEE/ACM TCBB, 2025) as features for determining pseudoalignment. We show that this scheme, which we call Finimap, leads to a significantly lower false-positive rate than other recent "approximate pseudoalignment" methods Kaminari and Raptor, and is also faster. Schloss Dagstuhl – Leibniz-Zentrum für Informatik Jarno N. Alanko and Elena Biagi and Simon J. Puglisi 2026 Is Part Of LIPIcs, Volume 390, 26th International Conference on Algorithms for Bioinformatics (WABI 2026) InProceedings Text doc-type:ResearchArticle publishedVersion application/pdf doi:10.4230/LIPIcs.WABI.2026.27 urn:nbn:de:0030-drops-275310 https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2026.27 eng https://creativecommons.org/licenses/by/4.0/legalcode