单分子实时测序
杂交基因组组装
基因组
计算生物学
Illumina染料测序
DNA测序
全基因组测序
工作流程
计算机科学
生物
有向无环图
霰弹枪测序
顺序装配
参考基因组
DNA
遗传学
算法
基因
DNA测序器
数据库
基因表达
转录组
作者
Chen-Shan Chin,David H. Alexander,Patrick Marks,Aaron A. Klammer,James Drake,Cheryl Heiner,Alicia Clum,Alex Copeland,John Huddleston,Evan E. Eichler,Stephen W. Turner,Jonas Korlach
出处
期刊:Nature Methods
[Springer Nature]
日期:2013-05-05
卷期号:10 (6): 563-569
被引量:3625
摘要
We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.
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