ArticleiMeta2023
EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research.
Article in iMeta, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers, 1 of them a synthesis that pooled it.
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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
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Who cites it
131 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities.Nature ecology & evolution · 2024Pooled it
- Oral microbiome dynamics in head and neck cancer patients undergoing oral healthcare: implications for prognosis and early diagnosis.BMC microbiology · 2025Trial
- Gut microbiota biomarkers of chronic kidney disease progression identified by 16S rDNA sequencing and machine learning.Renal failure · 2026Article
- Fecal Pathogenic Bacteria Composition and Community Assembly Mechanisms in Captive Brown Bears and Asiatic Black Bears.Animals : an open access journal from MDPI · 2026Article
- Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.The New phytologist · 2026Article
- Unraveling the coastal marine plastisphere archaeome.Nature communications · 2026Article
- Bacterial Communities Across the Production Chain of a Pacific Oyster (Pathogens (Basel, Switzerland) · 2026Article
- Review
- Host phylogeny and diet shape gut microbiome and virome in wild small mammals of Gongga Mountain, China.Zoological research · 2026Article
- Article
- Salt/alkali‑tolerant Streptomyces luteus TRM 45540 improves pepper growth and soil quality in acidic and alkaline soils.BMC plant biology · 2026Article
- Time-series dynamics and biocontrol potential of postharvest bacteria in litchi microbiota.Science China. Life sciences · 2026Article
- Transcriptome and 16S rRNA Amplicon Sequencing Analysis of Nutrition Metabolism in Silver Pomfret at Varying Flow Rates.Animals : an open access journal from MDPI · 2026Article
- Article
- Potential Role of Captive Environments in Reshaping the Compositions of Pathogenic Gut Bacteria inBiology · 2026Article
- Functional traits shape gut microbial assembly beyond phylogeny in estuarine fish.Science China. Life sciences · 2026Article
- Oropharyngeal Microbiota Associated with Sore Throat in Acute Upper Respiratory Tract Infections.Current microbiology · 2026Article
- Tissue-specific assembly of endophytic microbiota in Agriophyllum squarrosum (L.) Moq.BMC microbiology · 2026Article
- Behavioral smearing and physiological secretions drive divergent microbiome assembly during breeding in the crested ibis.Zoological research · 2026Article
- Multi-omics analysis reveals the critical role of gut microbiota related tryptophan and glutathione metabolism in sepsis-associated encephalopathy.BMC microbiology · 2026Article
71 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is difficult for beginners to learn and use amplicon analysis software because there are so many software tools to choose from, and all of them need multiple steps of operation. Herein, we provide a cross-platform, open-source, and community-supported analysis pipeline EasyAmplicon. EasyAmplicon has most of the modules needed for an amplicon analysis, including data quality control, merging of paired-end reads, dereplication, clustering or denoising, chimera detection, generation of feature tables, taxonomic diversity analysis, compositional analysis, biomarker discovery, and publication-quality visualization. EasyAmplicon includes more than 30 cross-platform modules and R packages commonly used in the field. All steps of the pipeline are integrated into RStudio, which reduces learning costs, keeps the flexibility of the analysis process, and facilitates personalized analysis. The pipeline is maintained and updated by the authors and editors of WeChat official account "Meta-genome." Our team will regularly release the latest tutorials both in Chinese and English, read the feedback from users, and provide help to them in the WeChat account and GitHub. The pipeline can be deployed on various platforms, and the installation time is less than half an hour. On an ordinary laptop, the whole analysis process for dozens of samples can be completed within 3 h. The pipeline is available at GitHub (https://github.com/YongxinLiu/EasyAmplicon) and Gitee (https://gitee.com/YongxinLiu/EasyAmplicon).
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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.