Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly.
Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly.
复制标题
DOI：
10.1016/j.cbpc.2011.05.012
复制
发表时间：
2012-01
期刊：
影响因子：
--
通讯作者：
Walter RB
中科院分区：
文献类型：
--
作者：
Garcia TI;Shen Y;Catchen J;Amores A;Schartl M;Postlethwait J;Walter RB
对于许多研究人员来说，下一代测序数据是回答以前无法解决的一类问题的关键。实现这些目标的重要且具有挑战性的步骤之一是将大量的短测序读段准确地组装成完整的核酸序列。对于使用非模型或野生系统的研究小组来说，由于缺乏预先存在的EST或基因组参考文库，短读段组装可能构成重大挑战。虽然许多出版物描述了测序和组装的整个过程，但很少有人讨论多少和什么类型的读段最适合组装的主题。该项目的目标是使用真实的世界数据来探索读取数量和短读取质量评分对所得从头组装的影响。使用几个不同大小和质量的短读段样品，我们以自动化的方式产生了许多组装体。我们观察了读取长度、读取质量和读取数量的属性如何影响所得组装体，并根据我们的真实数据集提供了一些一般性建议。
For many researchers, next generation sequencing data holds the key to answering a category of questions previously unassailable. One of the important and challenging steps in achieving these goals is accurately assembling the massive quantity of short sequencing reads into full nucleic acid sequences. For research groups working with non-model or wild systems, short read assembly can pose a significant challenge due to the lack of pre-existing EST or genome reference libraries. While many publications describe the overall process of sequencing and assembly, few address the topic of how many and what types of reads are best for assembly. The goal of this project was use real world data to explore the effects of read quantity and short read quality scores on the resulting de novo assemblies. Using several samples of short reads of various sizes and qualities we produced many assemblies in an automated manner. We observe how the properties of read length, read quality, and read quantity affect the resulting assemblies and provide some general recommendations based on our real-world data set.
登录
查看更多内容
影响因子：
10.7
作者：
Gibbons, John G.;Janson, Eric M.;Rokas, Antonis
通讯作者：
Rokas, Antonis
影响因子：
4
作者：
Barski, Artem;Zhao, Keji
通讯作者：
Zhao, Keji
影响因子：
1.7
作者：
Zhao, Xiaohong;Palmer, Lance E.;Wittenberg, Gayle M.
通讯作者：
Wittenberg, Gayle M.
影响因子：
3.7
作者：
Narzisi G;Mishra B
通讯作者：
Mishra B
影响因子：
5.8
作者：
Conesa, A;Götz, S;Robles, M
通讯作者：
Robles, M