KATKA: A KRAKEN-like tool with $k$ given at query time

Abstract

We describe a new tool, KATKA, that stores a phylogenetic tree $T$ such that later, given a pattern $P [1..m]$ 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 $1 \leq i \leq m - k + 1$. This is similar to KRAKEN's functionality but with $k$ given at query time instead of at construction time.