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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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ShadowRegression error estimation is incredibly slow #3

Closed jdidion closed 6 years ago

jdidion commented 7 years ago

Currently we call out to the R package for the calculations. It is research code and probably not optimized for performance. I should be reimplemented in cython.

jdidion commented 6 years ago

Closing this. The Wang et al. Shadow Regression method should be considered deprecated and will be removed in a future version, in favor of a native python or Cython implementation of the Zhu et al. cubic spline method: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1052-3 (or a better method, if one exists by the time I get around to implementing it).