ArticlePLoS computational biology2023
HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Ancient DNA reveals a family ossuary and long-distance migration on the Pacific coast before the Inca Empire.Nature communications · 2026Article
- Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis.Genome biology · 2026Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- The genetic history of Portugal over the past 5,000 years.Genome biology · 2025Article
- TBH1: 12 000-year-old human skeleton and projectile point shed light on demographics and mortality in Terminal Pleistocene Southeast Asia.Proceedings. Biological sciences · 2025Article
- Genetic transitions in the Neolithic and Bronze Age at Mas d'en Boixos (Catalonia, Spain).iScience · 2025Article
- Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population.Communications biology · 2025Article
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Article
- soibean: High-Resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs.Molecular biology and evolution · 2024Article
- mtDNA "nomenclutter" and its consequences on the interpretation of genetic data.BMC ecology and evolution · 2024Article
- Haplogrep 3 - an interactive haplogroup classification and analysis platform.Nucleic acids research · 2023Article
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Authors and funding
5 authors.
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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-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.
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