EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

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, opensource, and community-supported analysis pipeline EasyAmplicon. Easy-Amplicon 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).

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

“…To further confirm the difference assessed by LEfSe, we also performed two‐tailed unpaired Mann–Whitney U tests. Considering the effects of potential confounders, such as age, gender and ethnicity, a multivariable association analysis was performed using the linear model in R. The plots were visualized using the ggplot2 package in R and modified from EasyAmplicon 13 …”

“…Considering the effects of potential confounders, such as age, gender and ethnicity, a multivariable association analysis was performed using the linear model in R. The plots were visualized using the ggplot2 package in R and modified from EasyAmplicon. 13 To investigate the functional attributes of gut microbiome, valid reads were de novo assembled into contigs for each sample. All coding regions (CDS) of metagenomic contigs were predicted by MetaGeneMark v3.26.…”

Comprehensive Probiogenomics Analysis of the Commensal Escherichia Coli CEC15 as a Potential Probiotic Strain

“…Library preparation and sequencing were performed as described before [107]. Bioinformatic analysis were performed using the EasyAmplicon script [155] where the reads were merged, had the primers removed, were dereplicated, and the chimeras removed with VSEARCH [156], the processed reads were clustered in operational taxonomic units (OTUs) and analyzed by alpha and beta diversity with USEARCH [157]. The graphics and statistical analysis were generated from the EasyAmplicon script on R Studio.…”

Fungal-bacteria interactions provide shelter for bacteria in Caesarean section scar diverticulum

“…The first comparison uses the Kluskal-Wallis test, the second comparison uses the Wilcoxon test, and finally LDA is used to determine the difference, and the p value is corrected using fdr. The calculation and visualization of species diversity and abundance are executed by the EasyMicroPlot R package [25] and EasyAmplicon pipline [26]. Annotations were performed using the KO, COG, and CAZy databases to explore changes in enzyme family related to the microbiome.…”