Johnson Matthew G, Gardner Elliot M, Liu Yang, Medina Rafael, Goffinet Bernard, Shaw A Jonathan, Zerega Nyree J C, Wickett Norman J
Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA.
Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, Illinois 60022 USA; Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208 USA.
Appl Plant Sci. 2016 Jul 12;4(7). doi: 10.3732/apps.1600016. eCollection 2016 Jul.
Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).
HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.
HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.
利用通过目标富集产生的序列数据进行系统发育分析，需要将高通量序列读数重新组装成基因座，这带来了许多生物信息学挑战。我们开发了HybPiper，作为一个用户友好的平台，用于组装基因区域、提取外显子和内含子序列以及识别旁系同源基因拷贝。我们使用旨在靶向333个系统发育标记和桑科波罗蜜属中125个具有功能意义的基因的诱饵对HybPiper进行了测试。
HybPiper在三个阶段实现序列组装的并行执行：读数映射、重叠群组装和目标序列提取。该流程能够恢复波罗蜜属22个物种中所有基因的近乎完整的基因序列。HybPiper还在超过一半的系统发育标记中恢复了超过500 bp的非靶向内含子序列，并在波罗蜜属中识别出旁系同源基因拷贝。
HybPiper是为Linux和Mac OS X设计的，可在https://github.com/mossmatters/HybPiper上免费获取。
