Jarno Alanko

Abstract The minimizer of a k-mer is the smallest m-mer inside the k-mer according to some order relation < of the m-mers. Minimizers are often used as keys in hash tables in indexing tasks in metagenomics and pangenomics. The main weakness of minimizer-based indexing is the possibility of very frequently occurring minimzers, which can slow query times down significantly.

Abstract We develop a robust machine learning classifier using both linear and nonlinear models (i.e., LASSO logistic regression (LR) and random forests (RF)) to predict the phenotypic resistance of \emph{Mycobacterium tuberculosis} (MTB) for a broad range of antibiotic drugs. We use data from the CRyPTIC consortium to train our classifier, which consists of whole genome sequencing and antibiotic susceptibility testing (AST) phenotypic data for 13 different antibiotics.

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