ArticleInternational journal of molecular sciences2021
Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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.
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Who cites it
18 citing papers in PubMed.
- The Effect of Probiotics on Health in Pregnancy and Infants: A Randomized, Double-Blind, Placebo-Controlled Trial.Nutrients · 2025Trial
- Targeting gut microbiota with short-chain fructo-oligosaccharides prebiotic fibers to support metabolic health in overweight prediabetic adults: a randomized, double-blinded, placebo-controlled study.Frontiers in nutrition · 2025Trial
- Beneficial effects of a prebiotic-postbiotic supplement on digestive health and fecal microbiota in dogs and cats.Frontiers in veterinary science · 2026Article
- Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa.Applied and environmental microbiology · 2025Article
- AmpWrap: a one-line fully automated amplicon metabarcoding 16S and 18S rRNA gene analysis.Bioinformatics advances · 2025Article
- Article
- Article
- Gut Microbiota Comparison in Rectal Swabs Versus Stool Samples in Cats with Kidney Stones.Microorganisms · 2024Article
- A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.Molecular ecology resources · 2024Review
- Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea.Microorganisms · 2024Article
- Preventive effects of a nutraceutical mixture of berberine, citrus and apple extracts on metabolic disturbances in Zucker fatty rats.PloS one · 2024Article
- Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice.Scientific reports · 2023Article
- The Cynomolgus Macaque Intestinal Mycobiome Is Dominated by theJournal of fungi (Basel, Switzerland) · 2022Article
- Meta'omics: Challenges and Applications.International journal of molecular sciences · 2022Article
- Absence of Bacteria Permits Fungal Gut-To-Brain Translocation and Invasion in Germfree Mice but Ageing Alone Does Not Drive Pathobiont Expansion in Conventionally Raised Mice.Frontiers in aging neuroscience · 2022Article
- Dysbiosis of Gastric Mucosal Fungal Microbiota in the Gastric Cancer Microenvironment.Journal of immunology research · 2022Article
- Article
- Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs.Microorganisms · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.
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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.