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TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects
Abstract
ABSTRACT A new approach to assembling large, random shotgun sequencing projects has been developed. The TIGR Assembler overcomes several major obstacles to assembling such projects: the large number of pairwise comparisons required, the presence of repeat regions, chimeras introduced in the cloning process, and sequencing errors. A fast initial comparison of fragments based on oligonucleotide content is used to eliminate the need for a more sensitive comparison between most fragment pairs, thus greatly reducing computer search time. Potential repeat regions are recognized by determining which fragments have more potential overlaps than expected given a random distribution of fragments. Repeat regions are dealt with by increasing the match criteria stringency and by assembling these regions last so that maximum information from nonrepeat regions can be used. The algorithm also incorporates a number of constraints, such as clone length and the placement of sequences from the opposite ends of a clone. TIGR Assembler has been used to assemble the complete 1.8 Mbp Haemophilus influenzae (Fleischmann et al., 1995) and 0.58 Mbp Mycoplasma genitalium (Fraser et al., 1995) genomes.
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Citations
Cited by
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
The Minimal Gene Complement of Mycoplasma genitalium
Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. (1995) · Science · doi:10.1126/science.270.5235.397 · Cited by 2,545
Self-citationAn Eulerian path approach to DNA fragment assembly
Pevzner, P. A., Tang, H., & Waterman, M. S. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171285098 · Cited by 1,352
Mapping and sequencing of structural variation from eight human genomes
Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., et al. (2008) · Nature · doi:10.1038/nature06862 · Cited by 1,119
Metadata
- Authors
- SUTTON, G. G., WHITE, O., ADAMS, M. D., & KERLAVAGE, A. R.
- Venue
- Genome Science and Technology
- Publisher
- SAGE Publications
- Published
- 1995-01
- Volume
- 1
- Issue
- 1
- Pages
- 9-19
- ISSN
- 1070-2830 (ISSN-L)
- OpenAlex
- W2159497035
- Cited by
- 411
- References
- 0
- FWCI
- 3.43
- Type
- journal article
- Language
- en
- Open access
- closed
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- SUTTON, G. G., WHITE, O., ADAMS, M. D., & KERLAVAGE, A. R. (1995). TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects. Genome Science and Technology. https://doi.org/10.1089/gst.1995.1.9
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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
