Whole-genome shotgun assembly and comparison of human genome assemblies

Sorin Istrail, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, Brian Walenz, Hagit Shatkay, Ian Dew, Jason R. Miller, Michael J. Flanigan, Nathan J. Edwards, Randall Bolanos, Daniel Fasulo, Bjarni V. Halldorsson, Sridhar Hannenhalli, Russell Turner, Shibu Yooseph, Fu Lu, Deborah R. NusskernBixiong Chris Shue, Xiangqun Holly Zheng, Fei Zhong, Arthur L. Delcher, Daniel H. Huson, Saul A. Kravitz, Laurent Mouchard, Knut Reinert, Karin A. Remington, Andrew G. Clark, Michael S. Waterman, Evan E. Eichler, Mark D. Adams, Michael W. Hunkapiller, Eugene W. Myers, J. Craig Venter

Rannsóknarafurð: Framlag til fræðitímaritsGreinritrýni

144 Tilvitnanir (Scopus)

Útdráttur

We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and the inserts from which pairs of reads were obtained covered the genome 39 times. With the nearly complete human DNA sequence [National Center for Biotechnology Information (NCBI) Build 34] now available, it is possible to directly assess the quality, accuracy, and completeness of WGSA and of the first reconstructions of the human genome reported in two landmark papers in February 2001 [Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) Science 291, 1304-1351; International Human Genome Sequencing Consortium (2001) Nature 409, 860-921]. The analysis of WGSA shows 97% order and orientation agreement with NCBI Build 34, where most of the 3% of sequence out of order is due to scaffold placement problems as opposed to assembly errors within the scaffolds themselves. In addition, WGSA fills some of the remaining gaps in NCBI Build 34. The early genome sequences all covered about the same amount of the genome, but they did so in different ways. The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats.

Upprunalegt tungumálEnska
Síður (frá-til)1916-1921
Síðufjöldi6
FræðitímaritProceedings of the National Academy of Sciences of the United States of America
Bindi101
Númer tölublaðs7
DOI
ÚtgáfustaðaÚtgefið - 17 feb. 2004

Fingerprint

Sökktu þér í rannsóknarefni „Whole-genome shotgun assembly and comparison of human genome assemblies“. Saman myndar þetta einstakt fingrafar.

Vitna í þetta