Nephele: genotyping via complete composition vectors and MapReduce
2011
Nephele: A Tool for Genotyping Using Composition Vectors
Sample size: 155
publication
Evidence: high
Author Information
Author(s): Marc E. Colosimo, Matthew W. Peterson, Scott Mardis, Lynette Hirschman
Primary Institution: The MITRE Corporation
Hypothesis
Can Nephele improve the efficiency of genotyping using complete composition vectors and MapReduce?
Conclusion
Using Nephele can significantly reduce the time needed to generate genotype trees for large genomic datasets.
Supporting Evidence
- Nephele can generate a neighbour-joined tree of over 10,000 samples in less than 2 hours.
- The method produces results that correlate well with expert-defined genotypes.
- Execution times for individual gene segments ranged from 1.50 to 2.25 minutes, significantly faster than traditional methods.
Takeaway
Nephele is a computer program that helps scientists quickly group similar genetic sequences, making it easier to study diseases.
Methodology
Nephele uses complete composition vectors and affinity propagation clustering to analyze genetic sequences without traditional alignment methods.
Limitations
The study may be limited by the quality of the sequence data available in databases.
Digital Object Identifier (DOI)
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