ArticleGenome biology2025
X-Mapper: fast and accurate sequence alignment via gapped x-mers.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Author Correction: X-Mapper: fast and accurate sequence alignment via gapped x-mers.Genome biology · 2025Article
- Genomics insights of candidiasis: mechanisms of pathogenicity and drug resistance.Frontiers in microbiology · 2025Review
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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