De Novo Sequencing
The initial generation of the primary genetic sequence of a particular organism is called de novo sequencing. A detailed genetic analysis of any organism is possible only after de novo sequencing has been performed.
With its long read lengths and high accuracy, capillary electrophoresis-based sequencing is the gold standard technology for de novo projects. However, the throughput of these systems makes de novo assembly of most organisms a lengthy and costly endeavor. Next-generation sequencing technologies hold great promise in reducing the time and cost of sequencing.
De novo assembly of small organisms using the SOLiD™ System
The longer read lengths and new data analysis software of the SOLiD™ System enable the de novo assembly of small organisms. Researchers have demonstrated the assembly of 50bp reads into a scaffold that can then be filled in with capillary electrophoresis-based sequencing.
SOLiD™ System facilitates the assembly of difficult genomic regions.
For larger organisms, capillary electrophoresis-based sequencing is the preferred platform for scaffold generation. Once a scaffold is created the SOLiD™ System can be used to fill in the gaps at high coverage.
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Products
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Publications & Literature
Application Note
Poster
- Finding Indels with Short Sequencing Reads and De Novo Assembly
- Comparative Analysis of Salmonella Plasmids and Mobile Elements by Whole Genome Sequencing
- Distribution and Analysis of SPIs and Prophage Insertions in a Diverse Set of Salmonella Serogroups Sequenced by SOLiD™ System Technology
- Characterization of the ‘Mobilome’ of the genus Listeria
- Comparative Analysis of the rfb Locus, Encoding O-antigen Biosynthesis Genes in Salmonella enterica
Publication
- Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter Kashmirensis Ghosh W. et al, 2011, Journal of Bacteriology
- Whole Genome Sequencing of Environmental Vibrio Cholerae 01 from 10 Nanograms of DNA Using Short Reads Chaparro P. et al, 2011, Journal of Microbiological Methods
- Complete Genome Sequence of E. coli Journal Article
- First complete genome sequence of infectious laryngotracheitis virus Publication: BMC Genomics (2011)
- Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. Publication: Journal of Microbiological Methods (2011) Authors: Cerdeira L. et al.
For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.