Using quality scores and longer reads improves accuracy of Solexa read mapping.
Using quality scores and longer reads improves accuracy of Solexa read mapping.
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DOI：
10.1186/1471-2105-9-128
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发表时间：
2008-02-28
影响因子：
3
通讯作者：
Zhang MQ
中科院分区：
文献类型：
--
作者：
Smith AD;Xuan Z;Zhang MQ
第二代测序有可能彻底改变基因组学并影响生物医学的所有领域。测序技术的速度，灵敏度和可用性增加了对计算技术的进步，以执行相关的分析任务Solexa/Illumina 1G测序仪可以在一个实验中准确地映射到参考基因组中，几乎是所有应用程序的关键任务，可以产生数百万个读数。从Solexa技术绘制读取时，通常会忽略的是较长读取的3'端，其中包含更高的测序误差频率，以及基本通话质量得分。
为了调查这些信息源是否可以用于提高映射读取时的准确性，我们开发了RMAP工具，该工具可以映射读取具有较宽长度的读取，并允许基本计数质量得分来确定每个读取中的哪些位置更重要映射时。下载。
我们的结果表明，可以通过考虑较长的读取的3'端中的信息来实现Solexa读取映射性能，并适当使用我们开发的RMAP工具，使研究人员有效利用此信息。在有针对性的重新测量项目中。
Second-generation sequencing has the potential to revolutionize genomics and impact all areas of biomedical science. New technologies will make re-sequencing widely available for such applications as identifying genome variations or interrogating the oligonucleotide content of a large sample (e.g. ChIP-sequencing). The increase in speed, sensitivity and availability of sequencing technology brings demand for advances in computational technology to perform associated analysis tasks. The Solexa/Illumina 1G sequencer can produce tens of millions of reads, ranging in length from ~25–50 nt, in a single experiment. Accurately mapping the reads back to a reference genome is a critical task in almost all applications. Two sources of information that are often ignored when mapping reads from the Solexa technology are the 3' ends of longer reads, which contain a much higher frequency of sequencing errors, and the base-call quality scores. To investigate whether these sources of information can be used to improve accuracy when mapping reads, we developed the RMAP tool, which can map reads having a wide range of lengths and allows base-call quality scores to determine which positions in each read are more important when mapping. We applied RMAP to analyze data re-sequenced from two human BAC regions for varying read lengths, and varying criteria for use of quality scores. RMAP is freely available for downloading at . Our results indicate that significant gains in Solexa read mapping performance can be achieved by considering the information in 3' ends of longer reads, and appropriately using the base-call quality scores. The RMAP tool we have developed will enable researchers to effectively exploit this information in targeted re-sequencing projects.
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