KATKA: A KRAKEN-Like Tool with k Given at Query Time

Travis Gagie, Sana Kashgouli, Ben Langmead

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 \(1 \le i \le m - k + 1\). This is similar to KRAKEN’s functionality but with k given at query time instead of at construction time.