Nanopore duplex sequencing as an alternative to Illumina MiSeq sequencing for eDNA-based biomonitoring of coastal aquaculture impacts

Thorsten Stoeck; Sven Nicolai Katzenmeier; Hans-Werner Breiner; Verena Rubel

doi:10.3897/mbmg.8.121817

Research Article

Metabarcoding and Metagenomics 8: e121817
https://doi.org/10.3897/mbmg.8.121817 (29 May 2024)

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DOI: 10.1016/j.marpolbul.2025.118489

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DOI: 10.3389/fmars.2025.1688716

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DOI: 10.3390/ijms252312603

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Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade‐Offs in Resource‐Limited Settings. Molecular Ecology Resources 26: .

DOI: 10.1111/1755-0998.70091

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DOI: 10.1016/j.marpolbul.2024.117172

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DOI: 10.3390/ijms26104492

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DOI: 10.1111/jeu.70011

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DOI: 10.1038/s41598-025-18768-3

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DOI: 10.1007/978-981-95-2573-7_2

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