Australian marsupial phylogeny with denovo assembly of target exons captured sequences.. Australian marsupial phylogeny

Study focused on phylogeny of about 400 marsupial species collected in wide geographical region in Australia and Papua New Guinea. DNA specimens were used to preparing genomic library with following target exone capture enrichment and Illumina pair end short read sequencing (100bp PE) protocol. De novo assembly of targets was performed with TCCP (Target Capture Cloud Pipeline). This program performs musti-stage assembly based on Spades with automatic data cleanup and reads processing based on multiple bioinformatics tools: Picard tools, BBtools, BCFtools, Muscle, MACse, Diamond, Exonerate, IQtree, GATK.

本研究聚焦于约400种有袋类（marsupial）物种的系统发育学（phylogeny）分析，相关样本采集自澳大利亚与巴布亚新几内亚的广阔地理区域。研究采用DNA标本构建基因组文库，随后开展靶向外显子捕获富集，并遵循Illumina双端短读长测序（100bp PE）实验流程完成测序。针对靶标序列的从头组装（de novo assembly）工作通过TCCP（Target Capture Cloud Pipeline，靶向捕获云流程）完成，该程序基于SPAdes实现多阶段组装，并集成了Picard工具、BBtools、BCFtools、Muscle、MACSE、Diamond、Exonerate、IQ-TREE及GATK等多款生物信息学工具，可自动完成数据清理与读段处理。