转录本组装与质量评价.PDF

生 物 工 程 学 报 邓飞龙 等/转录本组装与质量评价 1271 Chinese Journal of Biotechnology /cjbcn September 25, 2015, 31(9): 1271−1278 DOI: 10.13345/j.cjb.140508 ©2015 Chin J Biotech, All rights reserved 综 述 转录本组装与质量评价 邓飞龙，贾先波，赖松家，刘益平，陈仕毅 四川农业大学 畜禽遗传资源发掘与创新利用四川省重点实验室，四川 成都 611130 邓飞龙, 贾先波, 赖松家, 等. 转录本组装与质量评价. 生物工程学报, 2015, 31(9): 1271–1278. Deng FL, Jia XB, Lai SJ, et al. Transcript assembly and quality assessment. Chin J Biotech, 2015, 31(9): 1271–1278. 摘 要: 转录本组装是基于第二代测序技术研究转录组的关键环节，其质量好坏直接影响到下游结果的可靠性， 也是目前的研究热点与难点。转录本组装方法可以分为Genome-guided 和de novo 两类，它们在理论基础与算法实 现方面各有优劣。转录本组装质量的高低依赖于PCR 扩增错误率、第二代测序技术准确率、组装算法和参考基因 组完整性等方面，而现有的算法还无法完全处理由这些因素带来的影响。本文从转录本组装方法与软件、影响组装 质量的因素和对组装质量的评价指标等方面进行讨论，以期能指导纯生物学家对分析软件的选择。 关键词: 转录组，第二代测序，组装软件，转录组测序 Transcript assembly and quality assessment Feilong Deng, Xianbo Jia, Songjia Lai, Yiping Liu, and Shiyi Chen Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China Abstract: The transcript assembly is essential for transcriptome studies from next-generation sequencing data. However, there are still many faults of algorithms in the present assemblers, which should be largely improved in the future. According to the requirement of reference genome or not, the transcript assembly could be classified into the genome-guided and de novo methods. The two methods have different algorithms and implementation processes. The quality of assembled transcripts depends on a large number of factors, such as the PCR amplificati