A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.

ABSTRACT:

Background

Adaptive sampling is an emerging technology to enrich target reads while depleting unwanted reads during real-time nanopore sequencing. The application of different algorithms has spawned various tools for the determination of read rejection. However, an evaluation in conjunction with identifying the optimal enrichment performance for a specific task has yet to be conducted.

Results

This study aimed to evaluate the performance of six widely used tools for nanopore adaptive sampling. Three distinct types of tasks were selected for testing, including the intraspecies enrichment of COSMIC genes, the interspecies enrichment of Saccharomyces cerevisiae, and the depletion of human host DNA. All the tools show increases in coverage depths of targets varying from 1.50- to

SUBMITTER: Yang L 

PROVIDER: S-EPMC12442282 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature