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

ABSTRACT:

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,

SUBMITTER: Navarro-Gomez D 

PROVIDER: S-EPMC4393525 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature