SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.

ABSTRACT: Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA (aDNA), is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C[Formula: see text]T and G[Formula: see text]A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y, respectively. This c

SUBMITTER: Rubin J 

PROVIDER: S-EPMC12693626 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature