Improving Rat Genome Assembly with Reliable Overlaps
Author Information
Author(s): Michael Roberts, Aleksey V. Zimin, Wayne Hayes, Brian R. Hunt, Cevat Ustun, James R. White, Paul Havlak, James Yorke
Primary Institution: Institute for Physical Science and Technology, University of Maryland
Hypothesis
Can the use of reliable overlaps improve the assembly quality of the rat genome?
Conclusion
The modified assembly method increased the coverage of finished sequence and significantly reduced the error rate.
Supporting Evidence
- The assembly increased the coverage of finished sequence from 93.4% to 96.3%.
- The base error rate was reduced from 4.5 to 1.1 errors per 10,000 bases.
- The assembly method was shown to be seven times better in overall quality.
Takeaway
This study shows a new way to put together the rat's DNA pieces more accurately, making fewer mistakes.
Methodology
The study used a modified version of the Phrap assembly program, called PhrapUMD, to create reliable overlaps for assembling the rat genome.
Limitations
The methods may not improve assembly for programs that do not use Phrap.
Digital Object Identifier (DOI)
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