|Publication Type||Journal Article|
|Year of Publication||2011|
|Authors||Gnerre, S, Maccallum, I, Przybylski, D, Ribeiro, FJ, Burton, JN, Walker, BJ, Sharpe, T, Hall, G, Shea, TP, Sykes, S, Berlin, AM, Aird, D, Costello, M, Daza, R, Williams, L, Nicol, R, Gnirke, A, Nusbaum, C, Lander, ES, Jaffe, DB|
|Journal||Proceedings of the National Academy of Sciences of the United States of America|
Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~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.