1.18(2023.2)

README.md

@@ -21,7 +21,7 @@ Popular software, scripts and database annotation for EasyAmplicon and EasyMetag
 	git clone https://github.com/YongxinLiu/EasyMicrobiome
 
 	# 方法2. 备用链接下载
-	wget -c http://210.75.224.110/db/EasyMicrobiome.zip
+	wget -c http://bailab.genetics.ac.cn/db/EasyMicrobiome.zip
 	unzip EasyMicrobiome.zip
 
 添加linux命令可执行权限
@@ -45,7 +45,7 @@ Popular software, scripts and database annotation for EasyAmplicon and EasyMetag
 
 流程的绘图部分，依赖的R包较多，推荐在Windows系统是使用(安装R包更方便)，同时提供了4百个包的合集下载，节省安装时间
 
-- R语言4.2环境和R包：R语言主页 http://www.r-project.org ，Windows版包合集 http://210.75.224.110/db/train/2107Amplicon12/win_soft/4.2.zip
+- R语言4.2环境和R包：R语言主页 http://www.r-project.org ，Windows版包合集 http://bailab.genetics.ac.cn/db/R/4.2.zip
 
 ## 软件清单
 
@@ -54,15 +54,15 @@ Popular software, scripts and database annotation for EasyAmplicon and EasyMetag
 - linux：Linux系统下分析软件
     - [microbiome_helper](https://github.com/LangilleLab/microbiome_helper)：微生物组分析输助脚本，如metaphlan2结果转换STAMP格式(metaphlan_to_stamp.pl)，picurst结果功能组成绘图(plot_metagenome_contributions.R)
     - Miniconda2-latest-Linux-x86_64.sh：软件管理器 https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
-    - qiime2-2022.2.tar.gz：QIIME2安装包，解压至conda的envs目录可用 http://210.75.224.110/db/conda/qiime2-2022.2.tar.gz
-    - qiime2-2022.2-py36-linux-conda.yml：QIIME2软件安装清单，使用conda在线安装
+    - qiime2-2022.11.tar.gz：QIIME2安装包，解压至conda的envs目录可用 http://bailab.genetics.ac.cn/db/conda/qiime2-2022.11.tar.gz
+    - qiime2-2022.11-py36-linux-conda.yml：QIIME2软件安装清单，使用conda在线安装
     - [sparcc](https://github.com/TankMermaid/sparcc)：sparcc网络分析python脚本
     - [usearch](http://www.drive5.com/usearch/)：扩增子分析流程
     - [vsearch](https://github.com/torognes/vsearch)：扩增子分析流程(免费64位版usearch)
 - mac：Mac系统下分析软件
     - csvtk：表格分析工具
     - iqtree：进化树构建
-    - qiime2-2022.2-py36-osx-conda.yml：QIIME2软件安装清单，使用conda在线安装
+    - qiime2-2022.11-py38-osx-conda.yml：QIIME2软件安装清单，使用conda在线安装
     - R-4.2.0.pkg：R语言安装包
     - RStudio-1.4.1106.dmg：RStudio安装包
     - rush：并行管理工具
@@ -74,7 +74,7 @@ Popular software, scripts and database annotation for EasyAmplicon and EasyMetag
     - [Git-2.30.2-64-bit.exe](http://gitforwindows.org/)：提供Git bash环境，自行下载安装，教程见：[Windows轻松实现linux shell环境：gitforwindows](https://mp.weixin.qq.com/s/KtM4c4o4iLfD4ZkEnMi1pg)
     - [R-4.2.0-win.exe](https://www.r-project.org/ )：R语言安装包，下载最新版：Downad CRAN - China Tsinghua - Download R for Windows(Mac) —— base —— Download R 4.2.0
     - [RStudio-1.4.1106.exe](https://www.rstudio.com/products/rstudio/download/#download)：RStudio安装包，提供分析运行界面。
-    - [4.2.zip](http://210.75.224.110/db/R/4.2.zip)：R语言常用400+包合集，解压至R包安装位置即可用。
+    - [4.2.zip](http://bailab.genetics.ac.cn/db/R/4.2.zip)：R语言常用400+包合集，解压至R包安装位置即可用。
     - [usearch.exe](http://www.drive5.com/usearch/)：扩增子分析流程
     - [vsearch.exe](https://github.com/torognes/vsearch)：扩增子分析流程(免费64位版usearch)
     - [STAMP2.1.3](http://kiwi.cs.dal.ca/Software/STAMP)：微生物组图形界面差异分析工具
@@ -100,9 +100,9 @@ Popular software, scripts and database annotation for EasyAmplicon and EasyMetag
 
 - gg：GreenGenes细菌16S数据库
     - [gg_13_8_otus.tar.gz](ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz
-)：13年8月更新OTU数据库，用于usearch有参定量和PICRUSt/BugBase功能预测、QIIME 2制作分类器。[国内备份链接](http://210.75.224.110/db/gg/gg_13_8_otus.tar.gz)
-    - [16S_13_5_precalculated.tab.gz](http://210.75.224.110/db/picrust/16S_13_5_precalculated.tab.gz)：picrust的GreenGenes 16S拷贝数
-	- [ko_13_5_precalculated.tab.gz](http://210.75.224.110/db/picrust/ko_13_5_precalculated.tab.gz)：picrust的GreenGenes 16S对应的KO数量信息
+)：13年8月更新OTU数据库，用于usearch有参定量和PICRUSt/BugBase功能预测、QIIME 2制作分类器。[国内备份链接](http://bailab.genetics.ac.cn/db/gg/gg_13_8_otus.tar.gz)
+    - [16S_13_5_precalculated.tab.gz](http://bailab.genetics.ac.cn/db/picrust/16S_13_5_precalculated.tab.gz)：picrust的GreenGenes 16S拷贝数
+	- [ko_13_5_precalculated.tab.gz](http://bailab.genetics.ac.cn/db/picrust/ko_13_5_precalculated.tab.gz)：picrust的GreenGenes 16S对应的KO数量信息
 - kegg：KEGG数据库描述信息整理
     - [ko00001.keg](https://www.kegg.jp)：KEGG层级注释体系，主页 —— KEGG BRITE —— KEGG Orthology (KO) —— Download htext，下载保存为ko00001.tsv
     - ko00001.tsv：转换jason格式为制表符分隔的KO对应描述、(三级)通路、二级通路和一级通路信息
@@ -166,8 +166,8 @@ Popular software, scripts and database annotation for EasyAmplicon and EasyMetag
 
 If used this script, please cited:
 
-Yong-Xin Liu, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Xu-Bo 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
+**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>, Tong Chen <chent@nrc.ac.cn>
+Copyright 2016-2023 Yong-Xin Liu <liuyongxin@caas.cn>, Tao Wen <taowen@njau.edu.cn>, Tong Chen <chent@nrc.ac.cn>
 
 

script/FAPROTAX_1.2.4/FAPROTAX.txt → script/FAPROTAX_1.2.6/FAPROTAX.txt

@@ -1,6 +1,6 @@
 # FAPROTAX: Functional Annotation of Prokaryotic Taxa
-# Version: 1.2.4
-# Copyright (c) 2020, Stilianos Louca
+# Version: 1.2.6
+# Copyright (c) 2022, Stilianos Louca
 #
 #
 #
@@ -6268,7 +6268,6 @@ aromatic_hydrocarbon_degradation			elements:C,H; main_element:C; electron_donor:
 *Mycobacterium*pyrenivorans*						# DOI:10.1099/ijs.0.03003-0
 *Flavobacteriales*Yeosuana*							# Garrity, Brenner, Krieg and Staley (2011) Bergey's Manual of Systematic Bacteriology, vol. 4
 *Flavobacteriaceae*Yeosuana*						# Garrity, Brenner, Krieg and Staley (2011) Bergey's Manual of Systematic Bacteriology, vol. 4. Legacy taxonomy
-*Geothrix*fermentans*								# DOI:10.1099/00207713-49-4-1615
 *Mycobacterium*frederiksbergense*					# Garrity, Brenner, Krieg and Staley (2012) Bergey's Manual of Systematic Bacteriology, vol. 5
 *Mycobacterium*fluoranthenivorans*					# Garrity, Brenner, Krieg and Staley (2012) Bergey's Manual of Systematic Bacteriology, vol. 5
 *Mycobacterium*hodleri*								# Garrity, Brenner, Krieg and Staley (2012) Bergey's Manual of Systematic Bacteriology, vol. 5
@@ -8620,8 +8619,6 @@ Roseospira*mediosalina*								# Garrity, Brenner, Krieg and Staley (2005) Berge
 *Proteobacteria*Herbaspirillum*						# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2
 *Oxalobacteraceae*Herbaspirillum*					# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2. Legacy taxonomy
 *Herbaspirillum*seropedicae*						# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2
-*Gammaproteobacteria*Massilia*						# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2
-*Oxalobacteraceae*Massilia*							# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2. Legacy taxonomy
 *Bordetella*bronchiseptica*							# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2
 *Bordetella*parapertussis*v							# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2
 *Ralstonia*paucula*									# Garrity, Brenner, Krieg and Staley (2005) Bergey's Manual of Systematic Bacteriology, vol. 2

script/FAPROTAX_1.2.4/README.txt → script/FAPROTAX_1.2.6/README.txt

@@ -37,7 +37,7 @@ If you need to modify the FAPROTAX database, for example to add new functional a
 
 LICENSE AGREEMENT
 - - - - - - - - -
-Copyright (c) 2020, Stilianos Louca
+Copyright (c) 2022, Stilianos Louca
 All rights reserved.
 
 Use and redistributions of the FAPROTAX database, including any associated software, with or without modification, are permitted provided that the following conditions are met: