CompleteCompositionVectorCLIA terminal-based app for genotyping via complete composition vectors and mapreduce | |
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CompleteCompositionVectorCLI Ranking & Summary
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- License:
- Apache
- Publisher Name:
- CompleteCompositionVectorCLI Team
- Publisher web site:
- http://code.google.com/u/102385706042576659077/
- Operating Systems:
- Mac OS X
- File Size:
- 26.7 MB
CompleteCompositionVectorCLI Tags
CompleteCompositionVectorCLI Description
The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, such methods are suboptimal for a rapidly growing dataset, because they require significant human effort, and because they increase in computational complexity quickly with the number of sequences. CompleteCompositionVectorCLI employs a method for genotyping which is independent of any multiple sequence alignment.CompleteCompositionVectorCLI uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods. Detailed instructions on how to install and use the CompleteCompositionVectorCLI utility on your Mac are available HERE.
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