Hybrid RY-mers increase aDNA alignment sensitivity

Hybrid RY-mers in the strobealign read aligner improve ancient DNA mapping accuracy and cut runtime by 4–6× versus BWA-aln on simulated genomic and metagenomic datasets.

• Why it matters: Accurate identification of endogenous short reads is a bottleneck in ancient DNA analysis, and general-purpose aligners can be too slow and insufficiently sensitive for highly divergent samples.
• What they did: The authors designed hybrid RY-mers to encode aDNA-specific sequence damage, integrated them into multi-context seeding, and tested strobealign on simulated genomic and metagenomic datasets.
• The result: Hybrid RY-mers increased mapping accuracy and reduced runtime by 4–6× versus BWA-aln, and replacing MALT in aMeta enabled faster, less memory-consuming detection of ancient taxa.

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