title: 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 form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at.
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Hansi
authors.initials: H
authors.lastname: Weissensteiner
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Dominic
authors.initials: D
authors.lastname: Pacher
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Anita
authors.initials: A
authors.lastname: Kloss-Brandstätter
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Lukas
authors.initials: L
authors.lastname: Forer
authors.affiliation: Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Günther
authors.initials: G
authors.lastname: Specht
authors.affiliation: Department of Mathematics, University of Hamburg, Hamburg 20146, Germany.
authors.forename: Hans-Jürgen
authors.initials: HJ
authors.lastname: Bandelt
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria.
authors.forename: Florian
authors.initials: F
authors.lastname: Kronenberg
authors.affiliation: Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, C.P. 15872, Galicia, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Salas
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck 6020, Austria sebastian.schoenherr@i-med.ac.at.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schönherr
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D008928:Mitochondria / Q000235:genetics; D010802:Phylogeny; D011786:Quality Control; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
chemical_list: D004272:DNA, Mitochondrial