ArticleScientific reports2021
Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.Microbiology spectrum · 2026Article
- Skin and gill microbiome profiles and network structures in farmed tilapia (Oreochromis niloticus) and their relationships with health conditions.Animal microbiome · 2025Article
- First isolation of a methanotrophicApplied and environmental microbiology · 2025Article
- Bacterial Diversity Dynamics in Sandy Loam Soils in Tanzania Under Varying Fertilizer-Derived Uranium Concentrations.Microorganisms · 2025Article
- Impacts of environmentally relevant concentrations of antibiotic cocktails on the skin microbiome of Eurasian carp (Cyprinus carpio).Animal microbiome · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Advancing time-since-interval estimation for clandestine graves: a forensic ecogenomics perspective into burial and translocation timelines using massively parallel sequencing.Frontiers in microbiology · 2025Review
- Next-generation sequencing applications in food science: fundamentals and recent advances.Frontiers in bioengineering and biotechnology · 2025Review
- Parental Reconstruction from a Half-Sib Population of Stoneless JujubePlants (Basel, Switzerland) · 2024Article
- Article
- Possible Shifts in the Genetic Diversity of Red-crowned Cranes (Animals : an open access journal from MDPI · 2024Article
- Characterization of the brain virome in human immunodeficiency virus infection and substance use disorder.PloS one · 2024Article
- Consumer identity but not food availability affects carabid diet in cereal crops.Journal of pest science · 2024Article
- Analysis of Crop Consumption Using Scatological Samples from the Red-Crowned CraneAnimals : an open access journal from MDPI · 2023Article
- Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications.Journal of AOAC International · 2023Article
- Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.Journal of molecular evolution · 2023Review
- A next-generation sequencing approach for the detection of mixed species in canned tuna.Food chemistry: X · 2023Article
- Laboratory protocol is important to improve the correlation between target copies and metabarcoding read numbers of seed DNA in ground beetle regurgitates.Scientific reports · 2023Article
- The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.Foods (Basel, Switzerland) · 2022Review
Corrections and comments
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4 authors.
Funding
Abstract
High-throughput sequencing platforms are increasingly being used for targeted amplicon sequencing because they enable cost-effective sequencing of large sample sets. For meaningful interpretation of targeted amplicon sequencing data and comparison between studies, it is critical that bioinformatic analyses do not introduce artefacts and rely on detailed protocols to ensure that all methods are properly performed and documented. The analysis of large sample sets and the use of predefined indexes create challenges, such as adjusting the sequencing depth across samples and taking sequencing errors or index hopping into account. However, the potential biases these factors introduce to high-throughput amplicon sequencing data sets and how they may be overcome have rarely been addressed. On the example of a nested metabarcoding analysis of 1920 carabid beetle regurgitates to assess plant feeding, we investigated: (i) the variation in sequencing depth of individually tagged samples and the effect of library preparation on the data output; (ii) the influence of sequencing errors within index regions and its consequences for demultiplexing; and (iii) the effect of index hopping. Our results demonstrate that despite library quantification, large variation in read counts and sequencing depth occurred among samples and that the sequencing error rate in bioinformatic software is essential for accurate adapter/primer trimming and demultiplexing. Moreover, setting an index hopping threshold to avoid incorrect assignment of samples is highly recommended.
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