The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Consed: A Graphical Tool for Sequence Finishing
Open accessAbstract
Sequencing of large clones or small genomes is generally done by the shotgun approach (Anderson et al. 1982). This has two phases: (1) a shotgun phase in which a number of reads are generated from random subclones and assembled into contigs, followed by (2) a directed, or finishing phase in which the assembly is inspected for correctness and for various kinds of data anomalies (such as contaminant reads, unremoved vector sequence, and chimeric or deleted reads), additional data are collected to close gaps and resolve low quality regions, and editing is performed to correct assembly or base-calling errors. Finishing is currently a bottleneck in large-scale sequencing efforts, and throughput gains will depend both on reducing the need for human intervention and making it as efficient as possible. We have developed a finishing tool, consed, which attempts to implement these principles. A distinguishing feature relative to other programs is the use of error probabilities from our programs phred and phrap as an objective criterion to guide the entire finishing process. More information is available at http://www.genome.washington.edu/consed/consed.html.
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Anderson, S., de Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F., & Young, I. G. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90137-1 · Cited by 1,472
Research works printed but not linked: 9
- 10.1093/nar/23.24.4992 · DOI
- 10.1073/pnas.83.11.3746 · DOI · Paper page
- 10.1093/nar/19.14.3907 · DOI · Paper page
- Dear, 1992, A standard file format for data from DNA sequencing instruments., DNA Sequence, 3, 107, 10.3109/10425179209034003 · DOI
- Ewing, B., L. Hillier, M. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. (this issue). · DOI
- 10.1093/nar/25.14.2745 · DOI · Paper page
- 10.1093/nar/18.21.6409 · DOI
- 10.1016/0022-2836(81)90087-5 · DOI · Paper page
- Swindell, 1997, SEQMAN: Contig assembly., Meth. Mol. Biol., 70, 75
Cited by
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
Self-citationCAP3: 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
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity
Markle, J. G. M., Frank, D. N., Mortin-Toth, S., Robertson, C. E., Feazel, L. M., Rolle-Kampczyk, U., von Bergen, M., McCoy, K. D., Macpherson, A. J., & Danska, J. S. (2013) · Science · doi:10.1126/science.1233521 · Cited by 2,025
Metadata
- Authors
- Gordon, D., Abajian, C., & Green, P.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1998-03-01
- Volume
- 8
- Issue
- 3
- Pages
- 195-202
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2164075646
- Cited by
- 3,302
- References
- 1
- Type
- posted content
- Language
- en
- Open access
- bronze
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