High-quality draft assemblies of mammalian genomes from massively parallel sequence data

被引：1150

作者：

Gnerre, Sante ^{[1
,2
]}

MacCallum, Iain ^{[1
,2
]}

Przybylski, Dariusz ^{[1
,2
]}

Ribeiro, Filipe J. ^{[1
,2
]}

Burton, Joshua N. ^{[1
,2
]}

Walker, Bruce J. ^{[1
,2
]}

Sharpe, Ted ^{[1
,2
]}

Hall, Giles ^{[1
,2
]}

Shea, Terrance P. ^{[1
,2
]}

Sykes, Sean ^{[1
,2
]}

Berlin, Aaron M. ^{[1
,2
]}

Aird, Daniel ^{[1
,2
]}

Costello, Maura ^{[1
,2
]}

Daza, Riza ^{[1
,2
]}

Williams, Louise ^{[1
,2
]}

Nicol, Robert ^{[1
,2
]}

Gnirke, Andreas ^{[1
,2
]}

Nusbaum, Chad ^{[1
,2
]}

Lander, Eric S. ^{[1
,2
,3
,4
]}

Jaffe, David B. ^{[1
,2
]}

机构：

[1] MIT, Broad Inst, Cambridge, MA 02142 USA

[2] Harvard Univ, Cambridge, MA 02142 USA

[3] MIT, Dept Biol, Cambridge, MA 02139 USA

[4] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA 02115 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2011年 / 108卷 / 04期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1073/pnas.1017351108

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：1513 / 1518

页数：6

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