转录本组装与质量评价

Transcript assembly and quality assessment

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。

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 amplification, sequencing techniques, assembly algorithm and genome character. Here, we reviewed the present tools of transcript assembly and various indexes for assessing the quality of assembled transcripts, which would help biologists to determine which assembler should be used in their studies.