1.21(2024.4)

.gitignore

@@ -1,4 +1,4 @@
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

Database_readme.txt

@@ -1,90 +1,90 @@
-Instructions for use:
-
-1. For the first time, please decompress the data files you need to use;
-2. If you need to use it frequently, it is recommended not to compress. Each compression and decompression will waste a lot of time; compression is only to save time during transmission;
-3. Before analysis, please visit the official database of each database to check whether there is an update of the database version;
-
-1. GreenGene database (gg)
-
-FTP address: ftp://greengenes.microbio.me/greengenes_release
-
-The latest version of the QIIME format database download link: 13_8 represents the update in August 2013
-
-ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz # 305 MB, updated on 2013/8/15, the sequence is the same as 13_5, only some species annotations are corrected
-
-After decompression, there are only three files in the 97 directory:
-
-97_otu_taxonomy.txt.gz # Species annotation of 97% cluster representative sequences, 1.2 MB
-97_otus.fasta.gz # 97% cluster representative sequence, 29 MB
-97_otus.tree.gz # Multiple sequence tree file of 97% cluster representative sequences, 929 KB
-
-
-2. USEARCH format database (usearch)
-
-Download page: http://www.drive5.com/sintax
-
-16S
-
-rdp_16s_v18.fa.gz # 20,000 sequences for genus annotation, newly version
-
-rdp_16s_v16_sp.fa.gz # 13,000 sequences for species annotation,
-
-silva_16s_v123.fa.gz # 1.6 million for removing chimeras to prevent false negatives. The more complete the chimera, the better
-
-
-3. UNITE database - ITS data
-
-Download page: https://unite.ut.ee/
-
-utax_reference_dataset_all_29.11.2022.fasta.gz # UNITE newly version fungal sequences and annotations
-
-The USEARCH data is a secondary arrangement and may not be updated in time. You can download the latest and full versions from the UNITE official website.
-
-If there is a problem, please refer to Appendix ## 11. UNITE database analysis error report in Pipeline.sh
-
-使用说明：
-
-1. 第一次使用请先解压缩需要用到的数据文件；
-2. 如果需要经常使用，建议不要压缩，每次压缩和解压会浪费很多时间；压缩只为在传输时节约时间；
-3. 分析前请访问各数据库官方，查询是否存在数据库版本的更新；
-
-一、GreenGene数据库(gg)
-
-FTP地址：ftp://greengenes.microbio.me/greengenes_release
-
-最新版 QIIME 格式数据库下载链接：13_8代表13年8月更新
-
-ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz # 305 MB, 2013/8/15更新，序列与13_5一致，只是修正部分物种注释
-
-解压后，通用只有97目录下的三个文件：
-
-97_otu_taxonomy.txt.gz  # 97%聚类代表序列的物种注释，1.2 MB
-97_otus.fasta.gz  # 97%聚类代表序列，29 MB
-97_otus.tree.gz # 97%聚类代表序列的多序列树文件，929 KB
-
-
-二、USEARCH格式数据库(usearch)
-
-下载页面：http://www.drive5.com/sintax
-
-16S
-
-	rdp_16s_v18.fa.gz # 20,000万条序列，用于物种注释
-
-	rdp_16s_v16_sp.fa.gz # 1.3万条序列，用于物种注释，物种注释是越准越好
-
-	silva_16s_v123.fa.gz # 160万条，用于去嵌合体，防止假阴性去除嵌合体是越全越好
-
-
-三、UNITE数据库 - ITS 数据
-
-下载页面：https://unite.ut.ee/
-
-	utax_reference_dataset_all_29.11.2022.fasta.gz # UNITE 最新版真菌序列及注释
-
-USEARCH数据是二次整理，不一定及时更新，可至UNITE官网下载最新版、完整版
-
-有问题，详见Pipeline.sh中附录 ## 11. UNITE数据库分析报错问题
-
-
-
+Instructions for use:
+
+1. For the first time, please decompress the data files you need to use;
+2. If you need to use it frequently, it is recommended not to compress. Each compression and decompression will waste a lot of time; compression is only to save time during transmission;
+3. Before analysis, please visit the official database of each database to check whether there is an update of the database version;
+
+1. GreenGene database (gg)
+
+FTP address: ftp://greengenes.microbio.me/greengenes_release
+
+The latest version of the QIIME format database download link: 13_8 represents the update in August 2013
+
+ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz # 305 MB, updated on 2013/8/15, the sequence is the same as 13_5, only some species annotations are corrected
+
+After decompression, there are only three files in the 97 directory:
+
+97_otu_taxonomy.txt.gz # Species annotation of 97% cluster representative sequences, 1.2 MB
+97_otus.fasta.gz # 97% cluster representative sequence, 29 MB
+97_otus.tree.gz # Multiple sequence tree file of 97% cluster representative sequences, 929 KB
+
+
+2. USEARCH format database (usearch)
+
+Download page: http://www.drive5.com/sintax
+
+16S
+
+rdp_16s_v18.fa.gz # 20,000 sequences for genus annotation, newly version
+
+rdp_16s_v16_sp.fa.gz # 13,000 sequences for species annotation,
+
+silva_16s_v123.fa.gz # 1.6 million for removing chimeras to prevent false negatives. The more complete the chimera, the better
+
+
+3. UNITE database - ITS data
+
+Download page: https://unite.ut.ee/
+
+utax_reference_dataset_all_29.11.2022.fasta.gz # UNITE newly version fungal sequences and annotations
+
+The USEARCH data is a secondary arrangement and may not be updated in time. You can download the latest and full versions from the UNITE official website.
+
+If there is a problem, please refer to Appendix ## 11. UNITE database analysis error report in Pipeline.sh
+
+使用说明：
+
+1. 第一次使用请先解压缩需要用到的数据文件；
+2. 如果需要经常使用，建议不要压缩，每次压缩和解压会浪费很多时间；压缩只为在传输时节约时间；
+3. 分析前请访问各数据库官方，查询是否存在数据库版本的更新；
+
+一、GreenGene数据库(gg)
+
+FTP地址：ftp://greengenes.microbio.me/greengenes_release
+
+最新版 QIIME 格式数据库下载链接：13_8代表13年8月更新
+
+ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz # 305 MB, 2013/8/15更新，序列与13_5一致，只是修正部分物种注释
+
+解压后，通用只有97目录下的三个文件：
+
+97_otu_taxonomy.txt.gz  # 97%聚类代表序列的物种注释，1.2 MB
+97_otus.fasta.gz  # 97%聚类代表序列，29 MB
+97_otus.tree.gz # 97%聚类代表序列的多序列树文件，929 KB
+
+
+二、USEARCH格式数据库(usearch)
+
+下载页面：http://www.drive5.com/sintax
+
+16S
+
+	rdp_16s_v18.fa.gz # 20,000万条序列，用于物种注释
+
+	rdp_16s_v16_sp.fa.gz # 1.3万条序列，用于物种注释，物种注释是越准越好
+
+	silva_16s_v123.fa.gz # 160万条，用于去嵌合体，防止假阴性去除嵌合体是越全越好
+
+
+三、UNITE数据库 - ITS 数据
+
+下载页面：https://unite.ut.ee/
+
+	utax_reference_dataset_all_29.11.2022.fasta.gz # UNITE 最新版真菌序列及注释
+
+USEARCH数据是二次整理，不一定及时更新，可至UNITE官网下载最新版、完整版
+
+有问题，详见Pipeline.sh中附录 ## 11. UNITE数据库分析报错问题
+
+
+

EasyAmplicon.Rproj

@@ -1,13 +1,13 @@
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-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX