Hybrid RY-mers increase aDNA alignment sensitivity
One of the key steps in ancient DNA data analysis is the accurate identification of endogenous short reads that originate from the ancient genome. Currently, this step is performed using general-purpose sequence aligners, such as BWA-aln, with parameter settings optimized for sensitivity. This approach results in increased runtime, even relative to standard DNA alignment workflows, and is not…
Ancient DNA data analysis relies on detecting endogenous short reads from ancient genomes, typically using general-purpose sequence aligners like BWA-aln. However, this method increases runtime and fails to align highly divergent samples from reference databases. To address this, the researchers introduce hybrid RY-mers, a seed construct that incorporates aDNA-specific sequence damage.
These hybrid RY-mers are adapted to the multi-context seeds concept and integrated into the read aligner strobealign. In simulated genomic and metagenomic datasets, hybrid RY-mers yield higher mapping accuracy while reducing runtime by 4-6 times compared to BWA-aln. Additionally, replacing the aDNA aligner MALT in the metagenomic tool-suite aMeta with the new alignment approach enables a faster and less memory-consuming detection of ancient taxa present in the samples.
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