KATKA: A KRAKEN-like tool with $k$ given at query time
Data Structures and Algorithms
2022-08-23 v2
Abstract
We describe a new tool, KATKA, that stores a phylogenetic tree such that later, given a pattern and an integer , it can quickly return the root of the smallest subtree of containing all the genomes in which the -mer occurs, for . This is similar to KRAKEN's functionality but with given at query time instead of at construction time.
Cite
@article{arxiv.2206.06053,
title = {KATKA: A KRAKEN-like tool with $k$ given at query time},
author = {Travis Gagie and Sana Kashgouli and Ben Langmead},
journal= {arXiv preprint arXiv:2206.06053},
year = {2022}
}