README.md

EasyAmplicon (易扩增子)

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

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

Version：v1.21

Update：2024/4/12

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 result data
• result/Diversity.Rmd # Interactive diversity 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 analyzing paired-end amplicon sequences.

Figure 2. Examples of publication-quality visualizations.

Figure 3. Supplementary examples of publication-quality visualizations to Figure 2.

Figure 4. Visualizations generated by third-party software using the intermediate files of EasyAmplicon.

Install (安装)

Install Dependency (安装依赖软件)

All the software backup can be found in

• FTP: Filezilla visiting FTP download.nmdc.cn in anonymous. In tools directory, you can find all the software and packages in amplicon and different system supporting such mac, win
• Baidu Net Disk：https://pan.baidu.com/s/1Ikd_47HHODOqC3Rcx6eJ6Q?pwd=0315

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/, also recommended install Rtools for install source code packages.

• RStudio 2023.xx.x is a integrated development environment for R https://posit.co/download/rstudio-desktop/

• STAMP v2.1.3 http://kiwi.cs.dal.ca/Software/STAMP

• Git for Windows 2.xx.x (Windows only) http://gitforwindows.org/

• 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 https://pan.baidu.com/s/1Ikd_47HHODOqC3Rcx6eJ6Q?pwd=0315 db/win/4.x.zip or db/mac/R4.2_mac_libraryX86_64.zip, then unzip and take the 4.x folder in C:\Users[$UserName]\AppData\Local\R\win-library\

Install EasyAmplicon (安装易扩增子)

• Method 1. Visit the GitHub homepage, Code -- Download

• 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 (keep the directoray name exact the software name)

• Method 2. Download by the mirror site in BaiduNetDisk: https://pan.baidu.com/s/1Ikd_47HHODOqC3Rcx6eJ6Q?pwd=0315 db/soft/EasyAmplicon.tar.gz or EasyMicrobiome.tar.gz

• 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:

1. Open RStudio, set termianl as Git Bash (Tools -- Global Options -- Terminal -- New termianls -- Git Bash -- OK)
2. File -- Open File -- EasyAmplicon folder -- pipeline.sh (windows/linux) or pipeline_mac.sh (mac)
3. 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 from 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)

使用此脚本，请引用下文：

If used this script, please cited:

Yong-Xin Liu, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Xubo Qian, Jiao Xi, Hongye Lu, Huiluo Cao, Xiaoya Ma, Bian Bian, Pengfan Zhang, Jiqiu Wu, Ren-You Gan, Baolei Jia, Linyang Sun, Zhicheng Ju, Yunyun Gao, Tao Wen, Tong Chen. 2023. EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research. iMeta 2: e83. https://doi.org/10.1002/imt2.83

Copyright 2016-2023 Yong-Xin Liu liuyongxin@caas.cn, Tao Wen taowen@njau.edu.cn, Tong Chen chent@nrc.ac.cn