Whole-genome shotgun assembly and comparison of human genome assemblies

@article{citeulike:2086064, abstract = {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. 10.1073/pnas.0307971100}, author = {Istrail, Sorin and Sutton, Granger G. and Florea, Liliana and Halpern, Aaron L. and Mobarry, Clark M. and Lippert, Ross and Walenz, Brian and Shatkay, Hagit and Dew, Ian and Miller, Jason R. and Flanigan, Michael J. and Edwards, Nathan J. and Bolanos, Randall and Fasulo, Daniel and Halldorsson, Bjarni V. and Hannenhalli, Sridhar and Turner, Russell and Yooseph, Shibu and Lu, Fu and Nusskern, Deborah R. and Shue, Bixiong C. and Zheng, Xiangqun H. and Zhong, Fei and Delcher, Arthur L. and Huson, Daniel H. and Kravitz, Saul A. and Mouchard, Laurent and Reinert, Knut and Remington, Karin A. and Clark, Andrew G. and Waterman, Michael S. and Eichler, Evan E. and Adams, Mark D. and Hunkapiller, Michael W. and Myers, Eugene W. and Venter, Craig J. }, citeulike-article-id = {2086064}, doi = {10.1073/pnas.0307971100}, journal = {Proceedings of the National Academy of Sciences}, keywords = {genome-assembly}, month = {February}, number = {7}, pages = {1916--1921}, posted-at = {2007-12-10 15:45:42}, priority = {2}, title = {Whole-genome shotgun assembly and comparison of human genome assemblies}, url = {http://dx.doi.org/10.1073/pnas.0307971100}, volume = {101}, year = {2004} }

TY - JOUR ID - citeulike:2086064 L3 - citeulike-article-id:2086064 TI - Whole-genome shotgun assembly and comparison of human genome assemblies JF - Proceedings of the National Academy of Sciences VL - 101 IS - 7 SP - 1916 EP - 1921 N2 - 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. 10.1073/pnas.0307971100 KW - genome-assembly AU - Istrail, Sorin AU - Sutton, Granger AU - Florea, Liliana AU - Halpern, Aaron AU - Mobarry, Clark AU - Lippert, Ross AU - Walenz, Brian AU - Shatkay, Hagit AU - Dew, Ian AU - Miller, Jason AU - Flanigan, Michael AU - Edwards, Nathan AU - Bolanos, Randall AU - Fasulo, Daniel AU - Halldorsson, Bjarni AU - Hannenhalli, Sridhar AU - Turner, Russell AU - Yooseph, Shibu AU - Lu, Fu AU - Nusskern, Deborah AU - Shue, Bixiong AU - Zheng, Xiangqun AU - Zhong, Fei AU - Delcher, Arthur AU - Huson, Daniel AU - Kravitz, Saul AU - Mouchard, Laurent AU - Reinert, Knut AU - Remington, Karin AU - Clark, Andrew AU - Waterman, Michael AU - Eichler, Evan AU - Adams, Mark AU - Hunkapiller, Michael AU - Myers, Eugene AU - Venter, Craig PY - 2004/02/17/ UR - http://dx.doi.org/10.1073/pnas.0307971100 ER -