SHRAP: A New Method for Genome Sequencing and Assembly
Author Information
Author(s): Sundquist Andreas, Ronaghi Mostafa, Tang Haixu, Pevzner Pavel, Batzoglou Serafim
Primary Institution: Stanford University
Hypothesis
Can high-throughput short-read technologies enable inexpensive de novo sequencing of mammalian genomes?
Conclusion
The SHRAP methodology demonstrates that inexpensive de novo sequencing of mammalian genomes is feasible using high-throughput, short-read technologies.
Supporting Evidence
- The SHRAP protocol allows for the assembly of complex genomes using short reads.
- Simulations showed that the methodology produces large contig sizes with relatively few misassemblies.
- Clone ordering and overlap detection are key components of the assembly process.
Takeaway
This study shows a new way to read and put together the DNA of animals, making it cheaper and easier to understand their genes.
Methodology
The study presents a sequencing protocol and assembly methodology called SHRAP, which uses high-throughput short-read technologies to assemble complex mammalian genomes.
Potential Biases
Potential biases in clone selection and sequencing errors could affect assembly quality.
Limitations
The methodology may not be suitable for small genomes and may face challenges with cloning bias and sequencing errors.
Digital Object Identifier (DOI)
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