ArticleiMetaOmics2024
Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis.
Article in iMetaOmics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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Who cites it
21 citing papers in PubMed.
- Oral microbiome dynamics in head and neck cancer patients undergoing oral healthcare: implications for prognosis and early diagnosis.BMC microbiology · 2025Trial
- Mechanically activated zinc oxide enhances growth performance and protects against diarrhea with potentially regulating gut microbiota in weaned piglets.Animal nutrition (Zhongguo xu mu shou yi xue hui) · 2026Article
- Unraveling the coastal marine plastisphere archaeome.Nature communications · 2026Article
- Partial replacement of corn and soybean meal with yeast culture improves growth performance and intestinal health and is associated with cecal microbiota modulation in broilers.Poultry science · 2026Article
- Review
- Wekemo Bioincloud 2026: An AI-enabled platform for standardized multi-omics data analyses.iMeta · 2026Article
- Time-series dynamics and biocontrol potential of postharvest bacteria in litchi microbiota.Science China. Life sciences · 2026Article
- Article
- Review
- Standardizing microbiome research: interlaboratory validation of SOPs for sample preparation and DNA extraction from food and environmental ecosystems.Environmental microbiome · 2025Article
- Article
- High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.NPJ biofilms and microbiomes · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Article
- MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics.iMeta · 2025Article
- Article
- Article
- Isobutyrate Confers Resistance to Inflammatory Bowel Disease through Host-Microbiota Interactions in Pigs.Research (Washington, D.C.) · 2025Article
- Ecological pattern of microalgal communities and associated risks in coastal ecosystems.ISME communications · 2025Article
- Correlation between oral microbiota and dry socket at different time periods on tooth extraction.Journal of oral microbiology · 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
39 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of next-generation sequencing has revolutionized microbiome research, enabling in-depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high-throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user-friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.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.