模块帮助文档

序列处理模块

• fastq数据统计　FASTQ Summary Statistics

• 原始数据碱基分布图　Draw nucleotides distribution chart

• 原始数据质量分布图　Draw quality score boxplot

• SE数据去低质量　Trimmomatic SE(single-end)

• PE数据去低质量　Trimmomatic PE(paired-end)

• fastq转fasta文件　Convert FASTQ to FASTA

• 计算fasta序列长度　Compute sequence length

• 按长度过滤fasta序列　Filter sequences by length

• fasta序列统计　Fasta Statistics

• PE数据拼接　Using FLASH to merge paired-end reads

• OTU聚类和丰度计算　Usearch otu cluster and mapping

• RDP分类学注释　RDP classifier assign taxonomy

• UTAX分类学注释　Usearch utax command assign taxonomy

标准分析模块

• 生成分组文件v1　Generate sample group file

• 生成分组文件v2　Generate sample group file from file header

• biom转table文件　Biom-To-Table

• table转biom文件　Table-To-Biom

• 转换table生成包含分类学的biom文件　Convert table to biom with taxonomy assignment information

• 生成对应分类学水平丰度表　Summary the representation of taxonomic groups

• 合并同组样品丰度　Merge Samples Abundance in same Group

• 标准化OTU Table　Normalize the OTU Table

• alpha指数计算　Alpha Diversity Index calculator

• 稀释性曲线　Plot samples rarefaction curves

• Shannon-Wiener曲线　Plot Shannon-Wiener rarefaction curves

• 分组均值稀释性曲线　Plot groups rarefaction curves

• Rank-Abundance曲线　Plot Rank Abundance curves

• 物种累计曲线　Plot Species Accumulation curves

• 群落结构柱状图　Community Bar Plot

• 群落结构饼图　Community Pie Plots

• 主成分分析　PCA analysis and plot PCA

• 3D散点图　3D Scatterplot

• 热图　Plot heatmap with tree

• 距离矩阵计算　Generate distance matrix

• 主坐标分析　PCOA analysis and plot PCOA

• NMDS分析　NMDS analysis and plot NMDS

• 层次聚类树　Plot hcluster tree

• 样本聚类树与柱状图组合分析　H Cluster Bar Plot

• 维恩图分析v1　Plot Venn Diagram

高级分析模块

• OTU表抽平　Creates a subsampled OTU table

• 各样品OTU个数和序列数统计　Summary OTU Table

• 合并同组丰度信息　Merge Samples Abundance in one Group

• 生成OTU子表　Get a sub-OTU Table

• 获取丰度最高的N个OTU   Select top N highest abundance rows in OTU/Taxon Table

• 丰度表过滤　Filter OTU/Taxon Table

• metastat丰度差异分析　Mothur-metastats command

• 过滤metastat分析结果　Filter Mothur-metastats Analysis Result

• R语言版本metastat分析　Metastats Analysis ( !!rather slow, not recommended )

• 秩和检验　Wilcoxon Test

• Anova检验　Anova Test

• 格式化LEfSe输入　LEfSe formatting

• LEfSe丰度差异分析　LDA Effect Size (LEfSe) Analysis

• 过滤LEfSe结果　Filter LEFSe result

• LEfSe LDA作图　Plot LEfSe Results

• LEfSe可视化圈图　Plot Cladogram

• LEfSe丰度差异bar图　Plot Differential Features

• DCA分析　DCA Analysis

• RDA分析　RDA Analysis

• CCA分析　CCA Analysis

• 获得对应分类学水平代表序列　Select representative seqs

• 代表序列系统发育树　Construt phylogenetic tree by OTU represent seqs

• 获得Unifrac距离矩阵　Get Unifrac Distance Matrix

• newick文件画树状图　Plot Tree

• 距离矩阵热图　Make Distance HeatMap

• 组间距离关系盒形图　Make Distance Boxplots

• ANOSIM检验　Runs the ANOSIM statistical method

• adonis检验　Runs the adonis statistical method

• Plsda分析　PLS-DA and plot Plsda

• 维恩图分析v2   Plot Venn Diagram

• 单样品分类学系统组成树　Single sample Taxonomy analysis tree

• 多样品分类学系统组成树　Multi samples Taxonomy analysis tree

• 克朗图　Plot Krona Pie Chart

其他分析模块

• GREENGENES分类学结果格式化　Process Tax Assign file

• fasta序列提取　Get Sequences from fasta file

• 合并fasta和qual得到fastq　Combine FASTA and QUAL