Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Next-generation sequencing has transformed microbiome research, necessitating automated and reproducible analysis pipelines.
• High-throughput microbiome data analysis requires significant bioinformatics expertise, limiting accessibility for many researchers.

Purpose of the Study:

• To introduce EasyAmplicon, a user-friendly bioinformatics pipeline for streamlined microbiome data analysis.
• To provide a detailed protocol and video tutorial for utilizing the EasyAmplicon pipeline, enhancing researcher accessibility.

Main Methods:

• Development of the EasyAmplicon pipeline integrating tools like USEARCH and VSEARCH.
• Implementation of automated workflows for data preprocessing, amplicon sequence variant analysis, diversity analysis, and visualization.
• Creation of a detailed protocol with video guidance for pipeline execution.

Main Results:

• EasyAmplicon offers a comprehensive, user-friendly solution for microbiome analysis.
• The pipeline automates complex steps, reducing the need for advanced bioinformatics skills.
• EasyAmplicon has achieved significant recognition, with 127 citations within its first year.

Conclusions:

• EasyAmplicon democratizes microbiome data analysis, making it accessible to a broader research community.
• The pipeline ensures automated, reproducible, and adaptable analysis of amplicon sequencing data.
• The freely available pipeline and detailed protocol support researchers in microbiome studies.