YongxinLiu / EasyAmplicon

Easy Amplicon data analysis pipeline
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EasyAmplicon

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:2024/08/05

Pipeline manual and file description

Using RStudio to open the pipeline available in Chinese (pipeline.sh) and English (pipeline_en.sh)

Files Description:

What can we do?

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Figure 1. The pipeline of EasyAmplicon for analyzing paired-end amplicon sequences.

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Figure 2. Examples of publication-quality visualizations.

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

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

Install

Install Dependency

All the software backups can be found in

Please install the dependency software according to your system (Win/Mac/Linux).

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

Download the project in C: or D: then unzip (keep the directory name exactly the software name)

Quick Start

Using Windows 10+ as an example:

  1. Open RStudio, and set the terminal as Git Bash (Tools -- Global Options -- Terminal -- New terminals -- 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 clicking run in the top right corner

Example dataset

FAQ

Frequently Asked Questions in pipeline.sh

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

Citation

If use this script, please cite:

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