IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar-Apr;15(2):494-505. doi: 10.1109/TCBB.2015.2446478.
New de novo transcriptome assembly and annotation methods provide an incredible opportunity to study the transcriptome of organisms that lack an assembled and annotated genome. There are currently a number of de novo transcriptome assembly methods, but it has been difficult to evaluate the quality of these assemblies. In order to assess the quality of the transcriptome assemblies, we composed a workflow of multiple quality check measurements that in combination provide a clear evaluation of the assembly performance. We presented novel transcriptome assemblies and functional annotations for Pacific Whiteleg Shrimp (Litopenaeus vannamei ), a mariculture species with great national and international interest, and no solid transcriptome/genome reference. We examined Pacific Whiteleg transcriptome assemblies via multiple metrics, and provide an improved gene annotation. Our investigations show that assessing the quality of an assembly purely based on the assembler's statistical measurements can be misleading; we propose a hybrid approach that consists of statistical quality checks and further biological-based evaluations.
新的从头转录组组装和注释方法为研究缺乏组装和注释基因组的生物体的转录组提供了一个极好的机会。目前有许多从头转录组组装方法，但评估这些组装的质量一直具有挑战性。为了评估转录组组装的质量，我们组合了多个质量检查措施的工作流程，这些措施结合起来可以清楚地评估组装的性能。我们为太平洋白对虾（Litopenaeus vannamei）提供了新颖的转录组组装和功能注释，太平洋白对虾是一种具有巨大国家和国际利益的海水养殖物种，没有可靠的转录组/基因组参考。我们通过多种指标检查了太平洋白对虾的转录组组装，并提供了改进的基因注释。我们的研究表明，仅仅基于组装者的统计测量来评估组装的质量可能会产生误导；我们提出了一种混合方法，包括统计质量检查和进一步的基于生物学的评估。
