EasyAmplicon (易扩增子)

The Chinese version in (中文版见) README_cn.md

An easy using, open-resource, reproducible, and community-based pipeline for amplicon data analysis in microbiome

Version：v1.18

Update：2023/2/3

Pipeline Manual and file description (流程使用和文件介绍)

Using RStudio open the pipeline.sh

Files description:

Readme.md # Introduction and install
pipeline.sh # Command-line analysis for Windows and Linux
pipeline_mac.sh # Command-line analysis for MacOS
result/ # Example data
result/Diversity.Rmd # Interactive analysis in R and output reproducible report in HTML format

What can we do? (结果展示)

Analysis and visualization of microbiome data, especially for 16S rDNA amplicon;
From raw data into feature tables;
Support 20+ analysis methods and publish-ready visualization;
Finish your project at your laptop in 3 hours;
Chinese/English manual and video supported.

Figure 1. Pipeline of EasyAmplicon for analysis pair-end amplicon data.

Figure 2. Examples of visualizations.

Install (安装)

Install Dependency (安装依赖软件)

Please install the dependency software according with you system (Win/Mac/Linux).

R 4.x.x for run R scripts https://www.r-project.org/
RStudio 2021.xx.x is a integrated development environment for R https://www.rstudio.com/products/rstudio/download/#download
STAMP v2.1.3 http://kiwi.cs.dal.ca/Software/STAMP
Git for Windows 2.xx.x (Windows only) http://gitforwindows.org/

As the windows users (87.5%) as example, you can quickly batch download above R 4.1.2, RStudio 2021.09.1, STAMP v2.1.3, Git 2.34.1 in zip.

R packages quick install

The statistics and visualization may require > 500 R packages. Installation is time-consuming and may also rely on other compilation tools. You can download all needed R packages in zip for windows or Mac, then unzip and take the 4.1 folder in C:\Users[$UserName]\Documents\R\win-library.

Install EasyAmplicon (安装易扩增子)

EasyAmplicon pipeline (Positive control) https://github.com/YongxinLiu/EasyAmplicon
EasyMicrobiome include scripts and databases https://github.com/YongxinLiu/EasyMicrobiome

Download the the project in C: or D:, then unzip (three methods keep always have backup)

Method 1. Visit the homepage, Code -- Download
Method 2. Download by the mirror site in China: EasyAmplicon EasyMicrobiome
Method 3. git clone https://github.com/YongxinLiu/EasyAmplicon and git clone https://github.com/YongxinLiu/EasyMicrobiome. Note: fatal: unable to access can retry.

Quick Start (快速运行)

Using Windows 10 as example:

Open RStudio, set termianl as Git Bash (Tools -- Global Options -- Terminal -- New termianls -- Git Bash -- OK)
File -- Open File -- EasyAmplicon folder -- pipeline.sh (windows/linux) or pipeline_mac.sh (mac)
Setup the work directory(wd), and EasyMicrobiome directory(db), then run each line by click run in top right corner

Example dataset (示例数据)

seq/ # raw sequencing in zipped fastq format, backup can download by metadata in GSA https://ngdc.cncb.ac.cn/gsa/
result/ # Example data and figures for standard pipeline, such as alpha, beta, tax
advanced/ # Example of advanced analysis, included data, scripts and output figures

FAQ (常见问题)

Frequenty Asked Questions in pipeline.sh

Note: All the .sh script is writting in markdown format, using Youdao Note or VSCode for better reading experience.

Citation (引文)

The paper is in submittion.

Please cite us review:

Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & Cell 12, 315-330, doi: https://doi.org/10.1007/s13238-020-00724-8

AntonioGPS/EasyAmplicon