Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier

D Navarro-Gomez, J Leipzig, LS Shen, M Lott, APM Stassen, DC Wallace, JL Wiggs, MJ Falk, Mannis Oven, XW Gai

Research output: Contribution to journalArticleAcademicpeer-review

45 Citations (Scopus)


Motivation: All current mitochondrial haplogroup classification tools require variants to be detected from an alignment with the reference sequence and to be properly named according to the canonical nomenclature standards for describing mitochondrial variants, before they can be compared with the haplogroup determining polymorphisms. With the emergence of high-throughput sequencing technologies and hence greater availability of mitochondrial genome sequences, there is a strong need for an automated haplogroup classification tool that is alignment-free and agnostic to reference sequence. Results: We have developed a novel mitochondrial genome haplogroup-defining algorithm using a k-mer approach namely Phy-Mer. Phy-Mer performs equally well as the leading haplogroup classifier, HaploGrep, while avoiding the errors that may occur when preparing variants to required formats and notations. We have further expanded Phy-Mer functionality such that next-generation sequencing data can be used directly as input.
Original languageUndefined/Unknown
Pages (from-to)1310-1312
Number of pages3
Issue number8
Publication statusPublished - 2015

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