ArticlePloS one2015
From benchtop to desktop: important considerations when designing amplicon sequencing workflows.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
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- Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.Molecular ecology resources · 2026Article
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- Moss-Accumulated eDNA Is a Promising Source for Terrestrial Biodiversity Surveys Across the Tree of Life and Biomes.Molecular ecology resources · 2026Article
- Identification of robust species-specific marker genes for the demarcation of theJournal of medical microbiology · 2025Article
- Airborne eDNA Reveals Resource-Based Assembly of Frugivorous Vertebrates.Molecular ecology resources · 2025Article
- Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research.Molecular ecology resources · 2025Article
- Observation Bias in Metabarcoding.Molecular ecology resources · 2025Article
- Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.Molecular ecology resources · 2025Article
- Design and Validation of an Open-Close Device for Integrated Environmental DNA Sampling Detects A Depth Gradient in Indian Ocean Deep-Sea Fish Assemblages.Ecology and evolution · 2025Article
- The Earth Hologenome Initiative: Data Release 1.GigaScience · 2025Article
- No pump, no problem: evaluating passive eDNA sampling for marine biomonitoring of a nuisance macroalga.PeerJ · 2025Article
- Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga.PloS one · 2025Article
- Validation of a species-specific probe-based qPCR for detection ofInternational journal for parasitology. Parasites and wildlife · 2024Article
- Effects of Polyvinyl Chloride (PVC) Microplastic Particles on Gut Microbiota Composition and Health Status in Rabbit Livestock.International journal of molecular sciences · 2024Article
- Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids.Ecology and evolution · 2024Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA) it is paramount workflows and analytics are both fit for purpose.
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