How does the efficiency of Nanopore compare to Illumina sequencing in tracking the spread of aquatic invasive species?

eDNA-based methods offer a non-invasive, easy-to-use approach for monitoring aquatic biodiversity, particularly for tracking invasive or cryptic species. While Illumina sequencing is commonly used, few studies have explored pairing eDNA sampling with Nanopore sequencing, a third-generation technology that allows for on-site sequencing but with a higher error rate. Here, we compared the performance of both technologies in detecting the invasive host-parasite complex Pseudorasbora parva-Sphaerothecum destruens. Water samples were collected from sites in Camargue and Corsica (Southern France), followed by DNA extraction, PCR amplification, and sequencing using either Illumina or Nanopore. Both technologies showed similar detection rates of P. parva , but only when Nanopore sequencing was performed under optimal conditions. However, for S. destruens , results varied: Illumina failed to detect the parasite, while Nanopore identified its DNA in multiple sites. We suggest that this discrepancy may be due to the different bioinformatic approaches used to process the reads and/or the higher error rate of Nanopore sequencing which could result in misassignments during species identification. • Illumina sequencing remains more efficient than Nanopore sequencing to detect species from eDNA samples. • Nanopore sequencing is less effective at assigning reads at a species level. • Detecting intracellular cryptic parasites using eDNA is challenging.