The Chinese version in (中文版见) README_cn.md
Version:v1.21
Update:2024/4/12
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
- 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.
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).
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R 4.x.x for run R scripts https://www.r-project.org/, also recommended install Rtools for install source code packages.
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RStudio 2023.xx.x is a integrated development environment for R https://posit.co/download/rstudio-desktop/
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STAMP v2.1.3 http://kiwi.cs.dal.ca/Software/STAMP
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Git for Windows 2.xx.x (Windows only) http://gitforwindows.org/
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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\
-
Method 1. Visit the GitHub homepage, Code -- Download
-
EasyAmplicon pipeline (Positive control) https://github.com/YongxinLiu/EasyAmplicon
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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
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Method 3.
git clone https://github.com/YongxinLiu/EasyAmplicon
andgit clone https://github.com/YongxinLiu/EasyMicrobiome
. Note:fatal: unable to access
can retry.
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), andEasyMicrobiome directory
(db), then run each line by click run in top right corner
- 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
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.
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 [email protected], Tao Wen [email protected], Tong Chen [email protected]