ReviewMolecular ecology resources2024
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.
Review in Molecular ecology resources, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 2 of them syntheses that pooled it.
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
31 citing papers in PubMed, 2 syntheses or guidelines pooled it, 71 citations in OpenAlex.
- Integrated Reanalysis of Global Riverine Fish eDNA Datasets Shows Robustness and Congruence of Biodiversity Conclusions.Molecular ecology · 2026Pooled it
- Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review.Parasites & vectors · 2024Pooled it
- Dive surveys and eDNA detect contrasting macroalgal community composition in Nova Scotia, Canada.Journal of phycology · 2026Article
- A Multilocus Nanopore eDNA Workflow for Red Algal Diversity Assessment in an Algal Reef System.Ecology and evolution · 2026Article
- A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.Molecular ecology resources · 2026Article
- Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use.Molecular ecology resources · 2026Article
- Phytoplankton Diversity in the Northern Adriatic Sea: Insights and Inconsistencies from Microscopy and Metabarcoding.Biology · 2026Article
- Assessing Prokaryotic Benthic Communities in the Red Sea.Environmental microbiology · 2026Article
- Optimization of environmental DNA-based methods: a case study for detecting brook trout (PeerJ · 2026Article
- Article
- A New Unsupervised Machine Learning Method for Metabarcoding Analysis Based on Selected Mock Community Data.Computational and structural biotechnology journal · 2026Article
- From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- QIIME2 pipeline for ITS2-based nemabiome sequencing in veterinary species and the importance of analysis parameters.Parasites & vectors · 2025Article
- DNA-Barcoding for Cultivar Identification and Intraspecific Diversity Analysis of Agricultural Crops.International journal of molecular sciences · 2025Review
- Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains.Applied and environmental microbiology · 2025Article
- A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018-2020.Molecular ecology resources · 2025Article
- From air to insight: the evolution of airborne DNA sequencing technologies.Microbiology (Reading, England) · 2025Review
- Metacommunity Theory and Metabarcoding Reveal the Environmental, Spatial and Biotic Drivers of Meiofaunal Communities in Sandy Beaches.Molecular ecology · 2025Article
- Comparative Analysis of Pasture Composition: DNA Metabarcoding Versus Quadrat-Based Botanical Surveys in Experimental Grassland Plots.Ecology and evolution · 2025Article
- Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.Molecular ecology resources · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
26 authors at 20 institutions in 13 countries.
Funding
Abstract
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
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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.