Fér Tomáš, Schmickl Roswitha E
Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic.
Evol Bioinform Online. 2018 Jan 12;14:1176934317742613. doi: 10.1177/1176934317742613. eCollection 2018.
Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of "quality-filtered" genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes.
The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/. HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications.
基于杂交的目标富集与基因组浅测序相结合（Hyb-Seq）正成为系统发育基因组学的标准方法。我们开发了HybPhyloMaker，这是一个生物信息学流程，可执行从原始读段到基于超级矩阵、超级树和多物种溯祖的物种树重建的目标富集数据分析。HybPhyloMaker用BASH编写并集成了常用的生物信息学工具。它既可以在本地运行，也可以在高性能计算机集群上运行。与现有的目标富集数据分析流程相比，HybPhyloMaker具有以下主要优势：实现了从原始读段到物种树重建的数据分析的所有步骤，计算和总结比对及基因树属性以帮助用户选择“质量过滤”基因，实现了多种物种树重建方法，以及对细胞器基因组编码区的分析。
HybPhyloMaker脚本、手册以及测试数据集可在https://github.com/tomas-fer/HybPhyloMaker/上获取。HybPhyloMaker根据开源许可GPL v.3授权，允许进一步修改。
