arXiv subjects

Sana Kashgouli

Publications and source records attributed to Sana Kashgouli.

2 recordsLinked to original sources

arXiv2022

MONI can find k-MEMs

Suppose we are asked to index a text $T [0..n - 1]$ such that, given a pattern $P [0..m - 1]$, we can quickly report the maximal substrings of $P$ that each occur in $T$ at least $k$ times. We first show how we can add $O (r \log n)$ bits to Rossi et al.'s recent MONI index, where $r$ is the number of runs in the Burrows-Wheeler Transform of $T$, such that it supports such queries in $O (k m \log n)$ time. We then show how, if we are given $k$ at construction time, we can reduce the query time to $O (m \log n)$.

cs.DS↗

arXiv2022

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

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.

cs.DS↗