The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
The Atlas Genome Assembly System
Open accessAbstract
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for dealing with repeated sequences. Inclusion of WGS sequences facilitates use of different clone insert sizes and reduces data production costs. A core function of Atlas software is recruitment of WGS sequences into appropriate BACs based on sequence overlaps. Because construction of consensus sequences is from local assembly of these reads, only small (<0.1%) units of the genome are assembled at a time. Once assembled, each BAC is used to derive a genomic layout. This “sequence-based” growth of the genome map has greater precision than with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects.
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Citations
Cites
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., et al. (1998) · Nature · doi:10.1038/31159 · Cited by 7,847
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins
Dehal, P., Satou, Y., Campbell, R. K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D. M., et al. (2002) · Science · doi:10.1126/science.1080049 · Cited by 1,641
Fast algorithms for large-scale genome alignment and comparison
Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036
Mullikin, J. C., & Ning, Z. (2003) · Genome Research · doi:10.1101/gr.731003 · Cited by 222
Cited by
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
The complete genome of an individual by massively parallel DNA sequencing
Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.-J., Makhijani, V., Roth, G. T., et al. (2008) · Nature · doi:10.1038/nature06884 · Cited by 1,838
Self-citationMinimus: a fast, lightweight genome assembler
Sommer, D. D., Delcher, A. L., Salzberg, S. L., & Pop, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-64 · Cited by 398
De novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204
Application of a superword array in genome assembly
Huang, X. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj419 · Cited by 30
Metadata
- Authors
- Havlak, P., Chen, R., Durbin, K. J., Egan, A., Ren, Y., Song, X.-Z., Weinstock, G. M., & Gibbs, R. A.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-04
- Volume
- 14
- Issue
- 4
- Pages
- 721-732
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W1984021931
- Cited by
- 180
- References
- 6
- Type
- posted content
- Language
- en
- Open access
- bronze
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