ArticleComputational and structural biotechnology journal2023
VTAM: A robust pipeline for validating metabarcoding data using controls.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Unravelling Bulk Ichthyoplankton Diversity in Vietnam: Metabarcoding Validation With Controlled Mock Samples.Molecular ecology resources · 2026Article
- Geographic Patterns of Intra- and Interspecific Diversity of Riverine Fish Species in the Italian Northern Apennines and Ligurian Alps.Ecology and evolution · 2026Article
- MitoNGS: an online platform to analyze fish metabarcoding data in high resolution.Molecular biology and evolution · 2026Article
- Disentangling the Effects of Biotic and Abiotic Dimensions of Ecological Opportunity on Individual Trophic Trait Variation.Molecular ecology · 2025Article
- A very picky eater: Species-level prey selection in the endangered Rhone streber [Zingel asper (L. 1758)].Journal of fish biology · 2025Article
- A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.Molecular ecology resources · 2024Review
- mkLTG: a command-line tool for taxonomic assignment of metabarcoding sequences using variable identity thresholds.Biologia futura · 2023Article
- Article
- DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish.Molecular ecology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To obtain accurate estimates for biodiversity and ecological studies, metabarcoding studies should be carefully designed to minimize both false positive (FP) and false negative (FN) occurrences. Internal controls (mock samples and negative controls), replicates, and overlapping markers allow controlling metabarcoding errors but current metabarcoding software packages do not explicitly integrate these additional experimental data to optimize filtering. We have developed the metabarcoding analysis software VTAM, which uses explicitly these elements of the experimental design to find optimal parameter settings that minimize FP and FN occurrences. VTAM showed similar sensitivity, but a higher precision compared to two other pipelines using three datasets and two different markers (COI, 16S). The stringent filtering procedure implemented in VTAM aims to produce robust metabarcoding data to obtain accurate ecological estimates and represents an important step towards a non-arbitrary and standardized validation of metabarcoding data for conducting ecological studies. VTAM is implemented in Python and available from: https://github.com/aitgon/vtam. The VTAM benchmark code is available from: https://github.com/aitgon/vtam_benchmark.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.