Aggressive assembly of pyrosequencing reads with mates.
Aggressive assembly of pyrosequencing reads with mates.
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DOI：
10.1093/bioinformatics/btn548
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发表时间：
2008-12-15
期刊：
影响因子：
5.8
通讯作者：
Sutton, Granger
中科院分区：
文献类型：
--
作者：
Miller, Jason R.;Delcher, Arthur L.;Koren, Sergey;Venter, Eli;Walenz, Brian P.;Brownley, Anushka;Johnson, Justin;Li, Kelvin;Mobarry, Clark;Sutton, Granger
动机：从Sanger和焦磷酸测序平台上读取DNA序列在成本、准确性、典型覆盖范围、平均读取长度和各种可用的配对端协议方面存在差异。在全基因组霰弹枪测序项目的“混合”方法中，这两种读取类型可以相互补充，但是组装软件必须修改以适应它们的不同特征。这甚至适用于焦磷酸测序的配对和未配对的读取组合。如果没有特殊的修改，为同构序列数据调优的汇编程序在混合数据上可能表现不佳。结果：Celera Assembler对ABI 3730和454 FLX reads的组合进行了修饰。改进后的管道称为CABOG（具有最佳重叠图的Celera Assembler），对均聚物运行长度的不确定性、高读取覆盖率和异构读取长度具有很强的稳稳性。在对四个基因组的测试中，它在所有测试的组装器中产生了最长的contigs。它利用来自两个平台的配对末端reads提供的配对约束来构建更大的contigs和scaffold，并通过与完成的参考序列的比较验证了这一点。在一些CABOG组合中检测到较低的连续错误装配率，但在有足够的配偶对数据的情况下，这一比例降低了。可用性：在GNU公共许可证下，该软件可以从http://wgs-assembler.sf.net免费获得开源。补充信息：补充数据可在Bioinformatics在线获取。
Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a ‘hybrid’ approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data. Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data. Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License. Contact: jmiller@jcvi.org Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
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DOI：
10.1073/pnas.0307971100
发表时间：
2004-02-17
影响因子：
11.1
作者：
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通讯作者：
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