Calling SNPs without a reference sequence.
Calling SNPs without a reference sequence.
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DOI：
10.1186/1471-2105-11-130
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发表时间：
2010-03-15
影响因子：
3
通讯作者：
Miller W
中科院分区：
文献类型：
--
作者：
Ratan A;Zhang Y;Hayes VM;Schuster SC;Miller W
下一代测序技术最常见的应用是重测序，其中将来自个体基因组的短读段与相同物种的参考基因组序列进行比对。然后，这些图谱可以用来识别群体中个体之间的遗传差异，并可能最终解释表型变异。已经报道了许多能够将短读段与参考比对并确定它们之间的差异的算法。关于如何使用这些技术来确定没有参考序列的物种个体之间的遗传差异的报道要少得多，这大大限制了可以容易地从这些新技术中受益的物种的数量。我们描述了一个计算管道，称为DIAL（从头识别等位基因），用于识别两个密切相关的基因组之间的单碱基取代，而无需参考基因组的帮助。即使当覆盖深度不足以从头组装时，该方法也有效，并且它可以扩展以确定小的插入/缺失。我们使用来自James沃森博士基因组的Roche/454序列数据（检测杂合位置）和最近来自猩猩的Illumina数据评估软件的有效性，在每种情况下，将我们的结果与使用参考基因组组装的计算分析结果进行比较。我们还说明了使用DIAL来识别转录组序列之间的核苷酸差异。DIAL可用于鉴定没有参考序列的物种中的核苷酸差异。我们的主要动机是使用这个工具来调查濒危物种的遗传多样性，因为所识别的序列差异可以用于设计基因分型阵列，以协助物种的管理。DIAL源代码可以在http://www.bx.psu.edu/miller_lab/上免费获得。
The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has been reported on how to use these technologies to determine genetic differences among individuals of a species for which a reference sequence is not available, which drastically limits the number of species that can easily benefit from these new technologies. We describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. We evaluate the software's effectiveness using published Roche/454 sequence data from the genome of Dr. James Watson (to detect heterozygous positions) and recent Illumina data from orangutan, in each case comparing our results to those from computational analysis that uses a reference genome assembly. We also illustrate the use of DIAL to identify nucleotide differences among transcriptome sequences. DIAL can be used for identification of nucleotide differences in species for which no reference sequence is available. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available at http://www.bx.psu.edu/miller_lab/.
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来自非常短的读物的新型细菌基因组的基因促进组装。
影响因子：
4.3
作者：
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通讯作者：
Lee, Vincent T.
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作者：
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通讯作者：
Durbin, Richard
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作者：
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通讯作者：
Lander, ES
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作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
46.9
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Gnirke A;Melnikov A;Maguire J;Rogov P;LeProust EM;Brockman W;Fennell T;Giannoukos G;Fisher S;Russ C;Gabriel S;Jaffe DB;Lander ES;Nusbaum C
通讯作者：
Nusbaum C