Details

Autor(en) / Beteiligte

• Rubin, Joshua Daniel
• Vogel, Nicola Alexandra
• Gopalakrishnan, Shyam
• Sackett, Peter Wad
• Renaud, Gabriel
• Noble, William Stafford

Titel

HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph

Ist Teil von

• PLoS computational biology, 2023-06, Vol.19 (6), p.e1011148-e1011148

Ort / Verlag

United States: Public Library of Science

Erscheinungsjahr

2023

Quelle

MEDLINE

Beschreibungen/Notizen

• 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-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.