SKiM: accurately classifying metagenomic ONT reads in limited memory.

ABSTRACT:

Motivation

Oxford Nanopore Technologies' devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing capabilities. Such capabilities create new challenges for metagenomic classifiers that must be computationally efficient yet robust enough to handle potentially erroneous DNA reads, while ideally inspecting only a few hundred bases of a read. Currently available DNA classifiers leave room for improvement with respect to classification accuracy, memory usage, and the ability to operate in targeted sequencing scenarios.

Results

We present SKiM: Short K-mers in Metagenomics, a new lightweight metagenomic classifier designed for ONT reads. Compared to state-of-the-art classifiers, SKiM requires only a fraction of memory to run, and can

SUBMITTER: Schneggenburger T 

PROVIDER: S-EPMC12502918 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature