Crystallizing short-read assemblies around seeds.
Crystallizing short-read assemblies around seeds.
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DOI：
10.1186/1471-2105-10-s1-s16
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发表时间：
2009-01-30
影响因子：
3
通讯作者：
Skiena S
中科院分区：
文献类型：
--
作者：
Hossain MS;Azimi N;Skiena S
新的短序列测序技术产生了大量的25-30碱基对末端序列。由此产生的reads与Sanger测序产生的特征有很大不同，并且需要与上一代序列组装器不同的方法。在本文中，我们提出了一个特别针对新的ABI SOLiD测序技术的短读从头组装程序。本文介绍了应用生物系统公司（Applied Biosystems）推出的新兴SOLiD平台上的真实数据，我们认为这是第一个从头开始的序列组装结果。我们的汇编器SHORTY使用极少量（5 - 10）长度为300 - 500bp的种子来增加短配对读取。这些种子使我们能够使用不超过100倍的短读覆盖率产生重要的组装，这可以在这些高容量测序仪的单次运行中获得。SHORTY利用了我们认为对短读组装社区感兴趣的两个想法：(1)使用单个种子读取来结晶组装；(2)准确估计多个跨成对端读取的互排距离。我们使用模拟的SOLiD数据展示了三种不同细菌物种的有效组装（N50 contig大小~40 kb）。序列工件限制了我们在真实数据上的性能，但是我们在这些数据上的结果比竞争的汇编器所取得的结果要好得多。
New short-read sequencing technologies produce enormous volumes of 25–30 base paired-end reads. The resulting reads have vastly different characteristics than produced by Sanger sequencing, and require different approaches than the previous generation of sequence assemblers. In this paper, we present a short-read de novo assembler particularly targeted at the new ABI SOLiD sequencing technology. This paper presents what we believe to be the first de novo sequence assembly results on real data from the emerging SOLiD platform, introduced by Applied Biosystems. Our assembler SHORTY augments short-paired reads using a trivially small number (5 – 10) of seeds of length 300 – 500 bp. These seeds enable us to produce significant assemblies using short-read coverage no more than 100×, which can be obtained in a single run of these high-capacity sequencers. SHORTY exploits two ideas which we believe to be of interest to the short-read assembly community: (1) using single seed reads to crystallize assemblies, and (2) estimating intercontig distances accurately from multiple spanning paired-end reads. We demonstrate effective assemblies (N50 contig sizes ~40 kb) of three different bacterial species using simulated SOLiD data. Sequencing artifacts limit our performance on real data, however our results on this data are substantially better than those achieved by competing assemblers.