title: Whole-genome shotgun assembly and comparison of human genome assemblies.
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.
authors.affiliation: Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA.
authors.forename: Sorin
authors.initials: S
authors.lastname: Istrail
authors.forename: Granger G
authors.initials: GG
authors.lastname: Sutton
authors.forename: Liliana
authors.initials: L
authors.lastname: Florea
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Halpern
authors.forename: Clark M
authors.initials: CM
authors.lastname: Mobarry
authors.forename: Ross
authors.initials: R
authors.lastname: Lippert
authors.forename: Brian
authors.initials: B
authors.lastname: Walenz
authors.forename: Hagit
authors.initials: H
authors.lastname: Shatkay
authors.forename: Ian
authors.initials: I
authors.lastname: Dew
authors.forename: Jason R
authors.initials: JR
authors.lastname: Miller
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Flanigan
authors.forename: Nathan J
authors.initials: NJ
authors.lastname: Edwards
authors.forename: Randall
authors.initials: R
authors.lastname: Bolanos
authors.forename: Daniel
authors.initials: D
authors.lastname: Fasulo
authors.forename: Bjarni V
authors.initials: BV
authors.lastname: Halldorsson
authors.forename: Sridhar
authors.initials: S
authors.lastname: Hannenhalli
authors.forename: Russell
authors.initials: R
authors.lastname: Turner
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.forename: Fu
authors.initials: F
authors.lastname: Lu
authors.forename: Deborah R
authors.initials: DR
authors.lastname: Nusskern
authors.forename: Bixiong Chris
authors.initials: BC
authors.lastname: Shue
authors.forename: Xiangqun Holly
authors.initials: XH
authors.lastname: Zheng
authors.forename: Fei
authors.initials: F
authors.lastname: Zhong
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
authors.forename: Saul A
authors.initials: SA
authors.lastname: Kravitz
authors.forename: Laurent
authors.initials: L
authors.lastname: Mouchard
authors.forename: Knut
authors.initials: K
authors.lastname: Reinert
authors.forename: Karin A
authors.initials: KA
authors.lastname: Remington
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Clark
authors.forename: Michael S
authors.initials: MS
authors.lastname: Waterman
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.forename: Mark D
authors.initials: MD
authors.lastname: Adams
authors.forename: Michael W
authors.initials: MW
authors.lastname: Hunkapiller
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Myers
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
mesh_terms: D019295:Computational Biology / Q000592:standards; D020451:Contig Mapping / Q000592:standards; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D012333:RNA, Messenger / Q000032:analysis; D012984:Software
chemical_list: D012333:RNA, Messenger