High-quality draft assemblies of mammalian genomes from massively parallel sequence data
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
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DOI：
10.1073/pnas.1017351108
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发表时间：
2011-01-25
影响因子：
11.1
通讯作者：
Jaffe, David B.
中科院分区：
文献类型：
--
作者：
Gnerre, Sante;MacCallum, Iain;Jaffe, David B.
大规模并行DNA测序技术通过以非常低的成本产生数十亿个相对较短（类似于100个碱基）的序列读取来彻底改变基因组学。虽然这些数据可以很容易地用于广泛的生物医学应用，但已证明难以使用它们来生成大型重复丰富的脊椎动物基因组的高质量从头基因组组装。到目前为止，从这些数据产生的基因组组装已经远远低于那些与旧的（但更昂贵的）毛细管测序方法获得的。在这里，我们报告了一种用于基因组组装的算法ALLPATHS-LG的开发，及其在Illumina平台上生成的来自人类和小鼠基因组的大规模并行DNA序列数据的应用。所得到的草图基因组组装具有良好的准确性、短程邻接性、长程连接性和基因组的覆盖率。特别地，碱基准确度高（>= 99.95%），并且支架尺寸（N50尺寸对于人= 11.5Mb，对于小鼠= 7.2Mb）接近用基于毛细管的测序获得的那些。改进的测序技术和改进的计算方法的结合现在应该可以显着增加大型基因组的从头测序。ALLPATHS-LG程序可在http://www.broadinstitute.org/science/programs/genome-biology/crd上获得。
Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (similar to 100-base) sequence reads at very low cost. Whereas such data can be readily used for a wide range of biomedical applications, it has proven difficult to use them to generate high-quality de novo genome assemblies of large, repeat-rich vertebrate genomes. To date, the genome assemblies generated from such data have fallen far short of those obtained with the older (but much more expensive) capillary-based sequencing approach. Here, we report the development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform. The resulting draft genome assemblies have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome. In particular, the base accuracy is high (>= 99.95%) and the scaffold sizes (N50 size = 11.5 Mb for human and 7.2 Mb for mouse) approach those obtained with capillary-based sequencing. The combination of improved sequencing technology and improved computational methods should now make it possible to increase dramatically the de novo sequencing of large genomes. The ALLPATHS-LG program is available at http://www.broadinstitute.org/science/programs/genome-biology/crd.