Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-Offs in Resource-Limited Settings.

ABSTRACT: Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges and improve accessibility, we directly compared multiple workflow components, including four DNA extraction methods, two primer sets, three Nanopore basecalling models, and two demultiplexing pipelines. Across 48 workflow combinations tested in an aquarium with 15 fish species, we mapped trade-offs between cost, sensitivity, and processing speed to assess where time and resource savings are possible without compromising detection. Workflows using the Qiagen Blood and Tissue (BT) extraction kit and amplification

SUBMITTER: Ip YCA 

PROVIDER: S-EPMC12760245 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature