X-Mapper: fast and accurate sequence alignment via gapped x-mers

Gaston, Jeffry M.; Alm, Eric J.; Zhang, An-Ni

X-Mapper: fast and accurate sequence alignment via gapped x-mers

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Author(s)

Gaston, Jeffry M.

•

Alm, Eric J.

•

Zhang, An-Ni

Date Issued

January 22, 2025

Journal

Genome Biology

Publisher

BioMed Central

Citation

Gaston, J.M., Alm, E.J. & Zhang, AN. X-Mapper: fast and accurate sequence alignment via gapped x-mers. Genome Biol 26, 15 (2025).

Version

Final published version

Abstract

Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, but more accurate with shorter seeds avoiding mutations. Here, we introduce X-Mapper, aiming to offer high speed and accuracy via dynamic-length seeds containing gaps, called gapped x-mers. We observe 11–24-fold fewer suboptimal alignments analyzing a human reference and 3–579-fold lower inconsistency across bacterial references than other aligners, improving on 53% and 30% of reads aligned to non-target strains and species, respectively. Other seed-based analysis algorithms might benefit from gapped x-mers too.

MIT Department

Massachusetts Institute of Technology. Department of Biological Engineering

Terms of Use

Creative Commons Attribution

https://creativecommons.org/licenses/by/4.0/

Persistent DSpace Link

https://hdl.handle.net/1721.1/158285

DOI of Published Version

https://doi.org/10.1186/s13059-024-03473-7