Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.

ABSTRACT: Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, w

SUBMITTER: Ravishankar S 

PROVIDER: S-EPMC11646131 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature