HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.
HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.
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DOI：
10.1093/nar/gkw233
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Schönherr S
中科院分区：
文献类型：
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作者：
Weissensteiner H;Pacher D;Kloss-Brandstätter A;Forer L;Specht G;Bandelt HJ;Kronenberg F;Salas A;Schönherr S
线粒体DNA(MtDNA)图谱可分为系统发育簇(单群组)，这在进化、法医学和医学遗传学中具有重要意义。随着总结已发表的线粒体DNA序列的潜在系统发育树的广泛增长，人工进行单倍群分类的过程将过于耗时。之前发布的分类工具HaploGrep提供了一种自动解决此问题的方法。在这里，我们介绍了完全更新的版本HaploGrep 2，它提供了几个高级功能，包括基于规则的通用系统，用于即时质量控制(QC)。这使得能够检测人工重组体和缺失的变异，以及注释罕见和幻影突变。此外，现在直接支持以VCF文件的形式处理高吞吐量数据。对于数据输出，实时生成多个图形报告，例如多序列比对格式、VCF格式和扩展的单群QC报告，所有这些都可以在应用程序中直接查看。此外，HaploGrep 2生成了相对于修订的剑桥参考序列编码的所有输入样本的可供发表的系统发育树。最后，新的距离度量和算法的优化提高了精度，加快了应用速度。HaploGrep 2可以在http://haplogrep.uibk.ac.at.上自由访问，无需任何注册
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.