HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph.

ABSTRACT: Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendl

SUBMITTER: Rubin JD 

PROVIDER: S-EPMC10281577 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature