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

TL;DR

KATKA is a new tool that efficiently identifies the smallest subtree containing genomes with specific k-mers, allowing k to be specified at query time, unlike prior tools like KRAKEN.

Contribution

It introduces a data structure enabling flexible k-mer queries in phylogenetic trees, with k specified at query time, enhancing KRAKEN's capabilities.

Findings

Supports rapid subtree identification for given k-mers

Allows k to be specified dynamically at query time

Improves flexibility over existing tools like KRAKEN

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.