High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.
High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.
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DOI：
10.1186/1471-2164-9-603
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发表时间：
2008-12-16
期刊：
影响因子：
4.4
通讯作者：
Wincker P
中科院分区：
文献类型：
--
作者：
Aury JM;Cruaud C;Barbe V;Rogier O;Mangenot S;Samson G;Poulain J;Anthouard V;Scarpelli C;Artiguenave F;Wincker P
大规模并行DNA测序仪器使得能够以比经典桑格技术显著更低的成本和更高的通量解码整个基因组。据估计，这些技术中的每一种都比标准方法产生具有更多问题特征的组件。这些问题根据所使用的技术而具有不同的性质。因此，适当的技术组合可能有助于解决大多数困难，并最终提供高质量的组件，而不需要任何基于桑格的输入。我们将使用桑格数据获得的组装与来自新测序技术的不同输入的组装进行了比较。将组装件与参考成品序列进行系统比较。我们发现，454 GSFLX在高覆盖率下使用时可以有效地产生高连续性。使用来自环化基因组片段的454个序列测试通过支架增强连续性的潜力。最后，我们探索使用Solexa-Illumina短读段通过实施一种技术来纠正454个共识错误来完善基因组草图。高质量的草案可以产生小基因组没有任何桑格数据输入。我们发现454 GSFLX和Solexa/Illumina在产生大重叠群和超重叠群方面表现出很大的互补性，错误率很低。
Massively parallel DNA sequencing instruments are enabling the decoding of whole genomes at significantly lower cost and higher throughput than classical Sanger technology. Each of these technologies have been estimated to yield assemblies with more problematic features than the standard method. These problems are of a different nature depending on the techniques used. So, an appropriate mix of technologies may help resolve most difficulties, and eventually provide assemblies of high quality without requiring any Sanger-based input. We compared assemblies obtained using Sanger data with those from different inputs from New Sequencing Technologies. The assemblies were systematically compared with a reference finished sequence. We found that the 454 GSFLX can efficiently produce high continuity when used at high coverage. The potential to enhance continuity by scaffolding was tested using 454 sequences from circularized genomic fragments. Finally, we explore the use of Solexa-Illumina short reads to polish the genome draft by implementing a technique to correct 454 consensus errors. High quality drafts can be produced for small genomes without any Sanger data input. We found that 454 GSFLX and Solexa/Illumina show great complementarity in producing large contigs and supercontigs with a low error rate.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
9.9
作者：
de Berardinis, Veronique;Vallenet, David;Castelli, Vanina;Besnard, Marielle;Pinet, Agnes;Cruaud, Corinne;Samair, Sumitta;Lechaplais, Christophe;Gyapay, Gabor;Richez, Celine;Durot, Maxime;Kreimeyer, Annett;Le Fevre, Francois;Schaechter, Vincent;Pezo, Valerie;Doering, Volker;Scarpelli, Claude;Medigue, Claudine;Cohen, Georges N.;Marliere, Philippe;Salanoubat, Marcel;Weissenbach, Jean
通讯作者：
Weissenbach, Jean
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
3
作者：
Smith AD;Xuan Z;Zhang MQ
通讯作者：
Zhang MQ
影响因子：
4.4
作者：
ROACH, JC;BOYSEN, C;HOOD, L
通讯作者：
HOOD, L