2022.3 v1.14

README.md

@@ -1,27 +1,38 @@
-# 易宏基因组(EasyMetagenome)——最简单易学易用的宏基因组分析流程
+# 易宏基因组——最简单易学易用的宏基因组分析流程 
+# EasyMetagenome - the easiest metagenome analysis workflow to learn and use
 
-版本：EasyMetagenome v1.11
+版本Version：v1.14
 
-更新时间：2021/5/7
+更新时间Update：2022/3/20
 
-## 文件介绍
+## 文件介绍File introduction
 
-- 1SoftDb.sh：软件和数据库安装
-- 2Pipeline.sh：分析流程
-- 3StatPlot.sh：统计和可视化代码
+- 0Install.sh：软件和数据库安装Software and database installation
+- 1Pipeline.sh：分析流程Analysis pipeline
+- 2StatPlot.sh：统计和可视化代码Statistics and visualization script
 
 Shell代码兼容Markdown格式，可使用有道云笔记中Markdown笔记中查看，有目录导航更方便浏览和阅读。
 
+The Shell code is compatible with the Markdown format, which can be viewed in the Markdown editor, such as YoudaoCloudNotes, VSCode, and the directory navigation is more convenient for browsing and reading.
+
 各文档附录部分为常见问题，供参考。
 
-## 使用方法
+The appendices of each document are frequently asked questions for reference.
+
+## 使用方法Instructions
+
+在64位版本系统，如Ubuntu 18.04/20.04+，CentOS7/8+的系统，按代码0，1，2逐步运行
 
-在64位版本系统，如Ubuntu 18.04/20.04，CentOS7/8的系统，按代码1，2，3逐步运行
+In 64-bit version system, such as Ubuntu 18.04/20.04+, CentOS7/8+ system, run step by step according to code 0, 1, 2.
 
 在命令行，或RStudio的Shell环境下使用，可以有道云笔记中显示代码目录，方便预览大纲
 
-## 引用
+Used in the command line or RStudio's Shell environment. You can display the code directory in Youdaoyun Notes, which is convenient for previewing the outline
+
+## 引用Citation
+
+使用此流程代码，请引用To use this scripts, please cite:
 
-使用此流程代码，请引用：
+**Tong Chen**, **Yong-Xin Liu**, Luqi Huang. 2022. ImageGP: An easy-to-use data visualization web server for scientific researchers. iMeta 1: e5. https://doi.org/10.1002/imt2.5
 
-Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai. (2021). A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & Cell 12, 315-330, doi: https://doi.org/10.1007/s13238-020-00724-8
+**Yong-Xin Liu**, Yuan Qin, **Tong Chen**, Meiping Lu, Xubo Qian, Xiaoxuan Guo, et al. 2021. A practical guide to amplicon and metagenomic analysis of microbiome data. **Protein & Cell** 12: 315-330. https://doi.org/10.1007/s13238-020-00724-8

binning/result/itol/annotation.txt

@@ -0,0 +1,10 @@
+ID	Kingdom	Phylum	Class	Order	Family	Genus	Species	score	completeness	contamination	strain_heterogeneity	size	N50	cluster_members
+mix_all.9	d__Bacteria	p__Firmicutes	c__Bacilli	o__Erysipelotrichales	f__Erysipelatoclostridiaceae	g__Erysipelatoclostridium	s__Erysipelatoclostridium sp000752095	51.12623879683389	60.19	2.38	50.0	1519794	1961	1
+s_ERR011348.2	d__Bacteria	p__Firmicutes_A	c__Clostridia	o__Oscillospirales	f__Acutalibacteraceae	g__Ruminococcus_E	s__Ruminococcus_E bromii_B	97.88723778390194	99.11	0.67	0.0	2044830	17967	3
+mix_all.4	d__Bacteria	p__Firmicutes_A	c__Clostridia	o__Oscillospirales	f__Acutalibacteraceae	g__CAG-177	s__CAG-177 sp003514385	49.83372202351667	58.71	2.43	66.67	1228061	2029	1
+mix_all.5	d__Bacteria	p__Firmicutes_A	c__Clostridia	o__Oscillospirales	f__Acutalibacteraceae	g__CAG-180	s__CAG-180 sp000432435	57.922352949106376	68.33	2.68	50.0	1150209	2017	1
+s_ERR011349.1	d__Bacteria	p__Firmicutes_A	c__Clostridia	o__TANB77	f__CAG-508	g__CAG-273	s__CAG-273 sp000435755	74.51366568136028	74.07	0.34	0.0	1266722	19379	2
+mix_all.8	d__Bacteria	p__Firmicutes_A	c__Clostridia	o__TANB77	f__CAG-465	g__CAG-465	s__CAG-465 sp000433755	43.293460566032884	53.67	2.67	50.0	1331228	1892	1
+mix_all.2	d__Bacteria	p__Firmicutes_A	c__Clostridia	o__Lachnospirales	f__Lachnospiraceae	g__Butyrivibrio_A	s__Butyrivibrio_A crossotus	86.57505764739355	85.57	0.22	100.0	2030996	5890	2
+mix_all.10	d__Bacteria	p__Firmicutes_C	c__Negativicutes	o__Acidaminococcales	f__Acidaminococcaceae	g__Phascolarctobacterium	s__Phascolarctobacterium faecium	40.103268739563454	54.42	3.33	21.43	1090128	1735	1
+mix_all.6	d__Bacteria	p__Bacteroidota	c__Bacteroidia	o__Bacteroidales	f__Bacteroidaceae	g__Bacteroides	s__Bacteroides uniformis	73.74557542187483	75.17	0.73	50.0	2932691	5262	2

binning/result/itol/genome.txt

@@ -0,0 +1,11 @@
+ID	score	completeness	contamination	strain_heterogeneity	size	N50	cluster_members
+mix_all.2	86.57505764739355	85.57	0.22	100.0	2030996	5890	2
+s_ERR011349.1	74.51366568136028	74.07	0.34	0.0	1266722	19379	2
+mix_all.8	43.293460566032884	53.67	2.67	50.0	1331228	1892	1
+mix_all.9	51.12623879683389	60.19	2.38	50.0	1519794	1961	1
+s_ERR011348.2	97.88723778390194	99.11	0.67	0.0	2044830	17967	3
+mix_all.6	73.74557542187483	75.17	0.73	50.0	2932691	5262	2
+mix_all.10	40.103268739563454	54.42	3.33	21.43	1090128	1735	1
+mix_all.4	49.83372202351667	58.71	2.43	66.67	1228061	2029	1
+mix_all.5	57.922352949106376	68.33	2.68	50.0	1150209	2017	1
+mix_all.7	92.33394276242433	94.49	0.8	0.0	1482666	4874	1

binning/result/itol/plan1/iTOL_colorstrip-Class.txt

@@ -0,0 +1,21 @@
+DATASET_COLORSTRIP
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#bebada
+DATASET_LABEL	Class
+LEGEND_COLORS	#a6cee3	#1f78b4	#b2df8a	#33a02c
+LEGEND_LABELS	c__Bacilli	c__Bacteroidia	c__Clostridia	c__Negativicutes
+LEGEND_SHAPES	1	1	1	1
+LEGEND_TITLE	Class
+MARGIN	5
+STRIP_WIDTH	25
+DATA
+mix_all.9	#a6cee3	c__Bacilli
+s_ERR011348.2	#b2df8a	c__Clostridia
+mix_all.4	#b2df8a	c__Clostridia
+mix_all.5	#b2df8a	c__Clostridia
+s_ERR011349.1	#b2df8a	c__Clostridia
+mix_all.8	#b2df8a	c__Clostridia
+mix_all.2	#b2df8a	c__Clostridia
+mix_all.10	#33a02c	c__Negativicutes
+mix_all.6	#1f78b4	c__Bacteroidia

binning/result/itol/plan1/iTOL_colorstrip-Family.txt

@@ -0,0 +1,21 @@
+DATASET_COLORSTRIP
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#bebada
+DATASET_LABEL	Family
+LEGEND_COLORS	#a6cee3	#1f78b4	#b2df8a	#33a02c	#fb9a99	#e31a1c	#fdbf6f
+LEGEND_LABELS	f__Acidaminococcaceae	f__Acutalibacteraceae	f__Bacteroidaceae	f__CAG-465	f__CAG-508	f__Erysipelatoclostridiaceae	f__Lachnospiraceae
+LEGEND_SHAPES	1	1	1	1	1	1	1
+LEGEND_TITLE	Family
+MARGIN	5
+STRIP_WIDTH	25
+DATA
+mix_all.9	#e31a1c	f__Erysipelatoclostridiaceae
+s_ERR011348.2	#1f78b4	f__Acutalibacteraceae
+mix_all.4	#1f78b4	f__Acutalibacteraceae
+mix_all.5	#1f78b4	f__Acutalibacteraceae
+s_ERR011349.1	#fb9a99	f__CAG-508
+mix_all.8	#33a02c	f__CAG-465
+mix_all.2	#fdbf6f	f__Lachnospiraceae
+mix_all.10	#a6cee3	f__Acidaminococcaceae
+mix_all.6	#b2df8a	f__Bacteroidaceae

binning/result/itol/plan1/iTOL_colorstrip-Genus.txt

@@ -0,0 +1,21 @@
+DATASET_COLORSTRIP
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#bebada
+DATASET_LABEL	Genus
+LEGEND_COLORS	#e41a1c	#377eb8	#4daf4a	#984ea3	#ff7f00	#ffff33	#a65628	#f781bf	#999999
+LEGEND_LABELS	g__Bacteroides	g__Butyrivibrio_A	g__CAG-177	g__CAG-180	g__CAG-273	g__CAG-465	g__Erysipelatoclostridium	g__Phascolarctobacterium	g__Ruminococcus_E
+LEGEND_SHAPES	1	1	1	1	1	1	1	1	1
+LEGEND_TITLE	Genus
+MARGIN	5
+STRIP_WIDTH	25
+DATA
+mix_all.9	#a65628	g__Erysipelatoclostridium
+s_ERR011348.2	#999999	g__Ruminococcus_E
+mix_all.4	#4daf4a	g__CAG-177
+mix_all.5	#984ea3	g__CAG-180
+s_ERR011349.1	#ff7f00	g__CAG-273
+mix_all.8	#ffff33	g__CAG-465
+mix_all.2	#377eb8	g__Butyrivibrio_A
+mix_all.10	#f781bf	g__Phascolarctobacterium
+mix_all.6	#e41a1c	g__Bacteroides

binning/result/itol/plan1/iTOL_colorstrip-Kingdom.txt

@@ -0,0 +1,21 @@
+DATASET_COLORSTRIP
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#bebada
+DATASET_LABEL	Kingdom
+LEGEND_COLORS	#1b9e77
+LEGEND_LABELS	d__Bacteria
+LEGEND_SHAPES	1
+LEGEND_TITLE	Kingdom
+MARGIN	5
+STRIP_WIDTH	25
+DATA
+mix_all.9	#1b9e77	d__Bacteria
+s_ERR011348.2	#1b9e77	d__Bacteria
+mix_all.4	#1b9e77	d__Bacteria
+mix_all.5	#1b9e77	d__Bacteria
+s_ERR011349.1	#1b9e77	d__Bacteria
+mix_all.8	#1b9e77	d__Bacteria
+mix_all.2	#1b9e77	d__Bacteria
+mix_all.10	#1b9e77	d__Bacteria
+mix_all.6	#1b9e77	d__Bacteria

binning/result/itol/plan1/iTOL_colorstrip-Order.txt

@@ -0,0 +1,21 @@
+DATASET_COLORSTRIP
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#bebada
+DATASET_LABEL	Order
+LEGEND_COLORS	#a6cee3	#1f78b4	#b2df8a	#33a02c	#fb9a99	#e31a1c
+LEGEND_LABELS	o__Acidaminococcales	o__Bacteroidales	o__Erysipelotrichales	o__Lachnospirales	o__Oscillospirales	o__TANB77
+LEGEND_SHAPES	1	1	1	1	1	1
+LEGEND_TITLE	Order
+MARGIN	5
+STRIP_WIDTH	25
+DATA
+mix_all.9	#b2df8a	o__Erysipelotrichales
+s_ERR011348.2	#fb9a99	o__Oscillospirales
+mix_all.4	#fb9a99	o__Oscillospirales
+mix_all.5	#fb9a99	o__Oscillospirales
+s_ERR011349.1	#e31a1c	o__TANB77
+mix_all.8	#e31a1c	o__TANB77
+mix_all.2	#33a02c	o__Lachnospirales
+mix_all.10	#a6cee3	o__Acidaminococcales
+mix_all.6	#1f78b4	o__Bacteroidales

binning/result/itol/plan1/iTOL_colorstrip-Phylum.txt

@@ -0,0 +1,21 @@
+DATASET_COLORSTRIP
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#bebada
+DATASET_LABEL	Phylum
+LEGEND_COLORS	#a6cee3	#1f78b4	#b2df8a	#33a02c
+LEGEND_LABELS	p__Bacteroidota	p__Firmicutes	p__Firmicutes_A	p__Firmicutes_C
+LEGEND_SHAPES	1	1	1	1
+LEGEND_TITLE	Phylum
+MARGIN	5
+STRIP_WIDTH	25
+DATA
+mix_all.9	#1f78b4	p__Firmicutes
+s_ERR011348.2	#b2df8a	p__Firmicutes_A
+mix_all.4	#b2df8a	p__Firmicutes_A
+mix_all.5	#b2df8a	p__Firmicutes_A
+s_ERR011349.1	#b2df8a	p__Firmicutes_A
+mix_all.8	#b2df8a	p__Firmicutes_A
+mix_all.2	#b2df8a	p__Firmicutes_A
+mix_all.10	#33a02c	p__Firmicutes_C
+mix_all.6	#a6cee3	p__Bacteroidota

binning/result/itol/plan1/iTOL_gradient-N50.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#ff7f00
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	N50
+LEGEND_COLORS	#e5e5e5	#ff7f00
+LEGEND_LABELS	Min. (1735.0)	Max. (19379.0)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	N50
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	1961
+s_ERR011348.2	17967
+mix_all.4	2029
+mix_all.5	2017
+s_ERR011349.1	19379
+mix_all.8	1892
+mix_all.2	5890
+mix_all.10	1735
+mix_all.6	5262

binning/result/itol/plan1/iTOL_gradient-cluster_members.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#1f78b4
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	cluster_members
+LEGEND_COLORS	#e5e5e5	#1f78b4
+LEGEND_LABELS	Min. (1.0)	Max. (3.0)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	cluster members
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	1
+s_ERR011348.2	3
+mix_all.4	1
+mix_all.5	1
+s_ERR011349.1	2
+mix_all.8	1
+mix_all.2	2
+mix_all.10	1
+mix_all.6	2

binning/result/itol/plan1/iTOL_gradient-completeness.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#e31a1c
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	completeness
+LEGEND_COLORS	#e5e5e5	#e31a1c
+LEGEND_LABELS	Min. (53.7)	Max. (99.1)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	completeness
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	60.19
+s_ERR011348.2	99.11
+mix_all.4	58.71
+mix_all.5	68.33
+s_ERR011349.1	74.07
+mix_all.8	53.67
+mix_all.2	85.57
+mix_all.10	54.42
+mix_all.6	75.17

binning/result/itol/plan1/iTOL_gradient-contamination.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#33a02c
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	contamination
+LEGEND_COLORS	#e5e5e5	#33a02c
+LEGEND_LABELS	Min. (0.2)	Max. (3.3)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	contamination
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	2.38
+s_ERR011348.2	0.67
+mix_all.4	2.43
+mix_all.5	2.68
+s_ERR011349.1	0.34
+mix_all.8	2.67
+mix_all.2	0.22
+mix_all.10	3.33
+mix_all.6	0.73

binning/result/itol/plan1/iTOL_gradient-score.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#1f78b4
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	score
+LEGEND_COLORS	#e5e5e5	#1f78b4
+LEGEND_LABELS	Min. (40.1)	Max. (97.9)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	score
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	51.1262387968339
+s_ERR011348.2	97.8872377839019
+mix_all.4	49.8337220235167
+mix_all.5	57.9223529491064
+s_ERR011349.1	74.5136656813603
+mix_all.8	43.2934605660329
+mix_all.2	86.5750576473935
+mix_all.10	40.1032687395635
+mix_all.6	73.7455754218748

binning/result/itol/plan1/iTOL_gradient-size.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#6a3d9a
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	size
+LEGEND_COLORS	#e5e5e5	#6a3d9a
+LEGEND_LABELS	Min. (1090128.0)	Max. (2932691.0)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	size
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	1519794
+s_ERR011348.2	2044830
+mix_all.4	1228061
+mix_all.5	1150209
+s_ERR011349.1	1266722
+mix_all.8	1331228
+mix_all.2	2030996
+mix_all.10	1090128
+mix_all.6	2932691

binning/result/itol/plan1/iTOL_gradient-strain_heterogeneity.txt

@@ -0,0 +1,23 @@
+DATASET_GRADIENT
+SEPARATOR TAB
+BORDER_WIDTH	0.5
+COLOR	#fb9a99
+COLOR_MAX	#b15928
+COLOR_MIN	#e5e5e5
+DATASET_LABEL	strain_heterogeneity
+LEGEND_COLORS	#e5e5e5	#b15928
+LEGEND_LABELS	Min. (0.0)	Max. (100.0)
+LEGEND_SHAPES	1	1
+LEGEND_TITLE	strain heterogeneity
+MARGIN	5
+STRIP_WIDTH	50
+DATA
+mix_all.9	50
+s_ERR011348.2	0
+mix_all.4	66.67
+mix_all.5	50
+s_ERR011349.1	0
+mix_all.8	50
+mix_all.2	100
+mix_all.10	21.43
+mix_all.6	50

binning/result/itol/plan1/iTOL_labels-Species.txt

@@ -0,0 +1,12 @@
+LABELS
+SEPARATOR TAB
+DATA
+mix_all.9	s__Erysipelatoclostridium sp000752095
+s_ERR011348.2	s__Ruminococcus_E bromii_B
+mix_all.4	s__CAG-177 sp003514385
+mix_all.5	s__CAG-180 sp000432435
+s_ERR011349.1	s__CAG-273 sp000435755
+mix_all.8	s__CAG-465 sp000433755
+mix_all.2	s__Butyrivibrio_A crossotus
+mix_all.10	s__Phascolarctobacterium faecium
+mix_all.6	s__Bacteroides uniformis