HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.

ABSTRACT: Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in fo

SUBMITTER: Weissensteiner H 

PROVIDER: S-EPMC4987869 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature