Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier
Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier
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DOI：
10.1093/bioinformatics/btu825
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发表时间：
2015-04-15
期刊：
影响因子：
5.8
通讯作者：
Gai, Xiaowu
中科院分区：
文献类型：
--
作者：
Navarro-Gomez, Daniel;Leipzig, Jeremy;Gai, Xiaowu
动机：当前所有的线粒体单倍群分类工具都要求在与参考序列比对中检测到变异，并根据描述线粒体变异的规范命名标准进行正确命名，然后才能与确定单倍群的多态性进行比较。随着高通量测序技术的出现以及线粒体基因组序列的更易获取，迫切需要一种无需比对且不依赖参考序列的自动化单倍群分类工具。
结果：我们使用k - 聚体方法（即Phy - Mer）开发了一种新的线粒体基因组单倍群定义算法。Phy - Mer的性能与领先的单倍群分类器HaploGrep相当，同时避免了在将变异准备为所需格式和符号时可能出现的错误。我们进一步扩展了Phy - Mer的功能，使得下一代测序数据可以直接用作输入。
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.