Gaussian Process based Bayesian Optimisation of NGS Assembly.
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Spearmint
bayehem
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README.md

README.md

BayeHem

Proof of concept of Bayesian hyperparameter optimisation for de novo transcriptome assembly.

Spearmint is used for this proof of concept as it was designed for object minimisation with as few runs as possible.

Using test transcriptome data from Trinity and estimating assembly likelihoods using RSEM-EVAL using the RNAspades assembler.

TODO

  • Actually get this running properly

  • Clean up code specifically make it generic enough to use

  • Do installation instructions