面向下一代测序技术的de novo序列拼接工具综述

Survey of de novoAssembly Tools for Next-generation Sequencing Technology

序列拼接是生物信息学的基础问题.全面总结了面向下一代测序技术的de novo DNA序列拼接工具,介绍下一代测序平台产生的数据特点以及de novo序列拼接算法所面临的挑战;给出序列拼接算法的形式化定义,总结目前最常用的拼接策略以及根据相应策略开发的拼接工具的特点和实现细节;对评估拼接性能的主要参数进行描述,并通过不同物种、不同规模的真实基因组序列数据对多个具有代表性的拼接工具进行测试,比较它们的拼接性能以验证相应的工具特点.为研究人员提供工具选择指导或改善拼接工具性能提供帮助;最后总结并阐述序列拼接工具存在的问题和发展趋势.

Sequence assembly is a basic research in bioinformatics.This paper provided a detail survey of de novo assembly tools for Next Generation Sequencing technology.Introduced the characteristic of data generated from Next Generation Sequencing platforms and the challenges of corresponding de novo assembly algorithm.Proposed formal definition of de novo assembly,common assembly tools base on different assembly strategies were analyzed and their characteristic and realization detail were described.Described the main evaluation parameter of assembly performance and compared some typical tools based on several experimental DNA sequences of different size and from different species to verify the tool′s characteristics,which offers a tentative guide for tools selection or supply an idea of tools improvement for bioinformatics researcher.Finally,it made a summarization and identified the problems to be solved and the new directions.