Unravelling reference bias in ancient DNA datasets.

ABSTRACT:

Motivation

The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the imp

SUBMITTER: Dolenz S 

PROVIDER: S-EPMC11254355 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature