Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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DOI：
10.1038/nmeth.2474
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发表时间：
2013-06-01
期刊：
影响因子：
48
通讯作者：
Korlach, Jonas
中科院分区：
文献类型：
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作者：
Chin, Chen-Shan;Alexander, David H.;Korlach, Jonas
我们提出了一个层次的基因组组装过程（HGAP）的高品质从头微生物基因组组装使用一个单一的，长插入鸟枪DNA文库结合单分子，实时（SMRT）DNA测序。我们的方法使用最长的读段作为种子来招募所有其他读段，以通过基于有向无环图的共识程序构建高度准确的预组装读段，我们使用现成的长读段组装器进行组装。与混合方法相比，HGAP不需要高度准确的原始读数进行纠错。我们证明了几种微生物的高效基因组组装使用少至三个SMRT细胞零模式波导阵列的测序和BAC使用一个SMRT细胞。使用此工作流程可以成功解析长重复区域。我们还描述了一个共识算法，采用SMRT测序的主要质量值，以产生从头基因组序列超过99.999%的准确性。
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.