KATKA: A KRAKEN-like tool with k given at query time
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We describe a new tool, KATKA, that stores a phylogenetic tree T such that later, given a query P and an integer k, it can quickly return the root of the smallest subtree of T containing all the genomes in which the k-mer P [i..i + k - 1] occurs, for 1 ≤ i ≤ m - k + 1. This is similar to KRAKEN's functionality but with k given at query time instead of at construction time.
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