基于总出现频率过滤,去掉低丰度序列,或筛选一定丰度的序列,比如说将频率低于1500的序列去掉,包括两个参数,最高和最低频率
The --p-min-frequency
and --p-max-frequency
can be combined to filter based on lower and upper limits of total frequency
这里只给了一个最低频率的限制。
qiime feature-table filter-samples \
--i-table table.qza \
--p-min-frequency 1500 \
--o-filtered-table sample-frequency-filtered-table.qza
基于出现的偶然性的过滤???Contingency-based filtering,也就是最少在多少个样品中都需要出现,通量有最高和最低频率设定: --p-min-features
and --p-min-samples。
qiime feature-table filter-features \
--i-table table.qza \
--p-min-samples 2 \
--o-filtered-table sample-contingency-filtered-table.qza
字段筛选Identifier-based filtering, 也就是保留哪些特征数据内容。
qiime feature-table filter-samples \
--i-table table.qza \
--m-metadata-file samples-to-keep.tsv \
--o-filtered-table id-filtered-table.qza
同样还有很多其他的筛选方式:
Metadata-based filtering
Taxonomy-based filtering of tables and sequences
序列过滤Filtering sequences
比如说这里根据原序列文件和分类文件提取mitochondria,chloroplast这两个门水平的序列文件。
qiime taxa filter-seqs \
--i-sequences sequences.qza \
--i-taxonomy taxonomy.qza \
--p-include p__ \
--p-exclude mitochondria,chloroplast \
--o-filtered-sequences sequences-with-phyla-no-mitochondria-no-chloroplast.qza
Filtering distance matrices
qiime diversity filter-distance-matrix \
--i-distance-matrix distance-matrix.qza \
--m-metadata-file samples-to-keep.tsv \
--o-filtered-distance-matrix identifier-filtered-distance-matrix.qza
qiime diversity filter-distance-matrix \
--i-distance-matrix distance-matrix.qza \
--m-metadata-file sample-metadata.tsv \
--p-where "[subject]='subject-2'" \
--o-filtered-distance-matrix subject-2-filtered-distance-matrix.qza
5、重要参考数据库
这个不多说了吧,大家按使用需求来下载,后面逐步会用到:
Data resources — QIIME 2 2023.9.2 documentation
6、各个插件模块使用
不熟悉的先查看help信息和官网介绍:
q2-alignment 是 QIIME 2 生态系统中的一个插件,用于对生物信息学序列数据进行比对和序列比较的工具。它可以用于将不同样本中的序列进行比对,分析它们之间的相似性和差异性。q2-alignment 提供了一些常用的比对算法和工具,使用户能够对序列进行比对、生成比对结果和后续的分析。
以下是 q2-alignment 插件的一些主要功能和使用方法:
功能和用途:
- 序列比对:对DNA、RNA或蛋白质序列进行比对。
- 多序列比对:能够处理多个序列文件,比对它们之间的相似性。
- 生成比对结果:产生比对结果,以便后续分析或可视化。
- 支持多种比对算法:包括常用的比对算法,如BLAST、MUSCLE、MAFFT 等。
qiime alignment --help
Usage: qiime alignment [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin provides support for generating and
manipulating sequence alignments.
Plugin website: https://github.com/qiime2/q2-alignment
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
mafft De novo multiple sequence alignment with MAFFT
mafft-add Add sequences to multiple sequence alignment with MAFFT.
mask Positional conservation and gap filtering.
# 运行比对(示例使用 MAFFT)
qiime alignment mafft \
--i-sequences sequences.qza \
--o-alignment aligned_sequences.qza
用于进行组成分析,尤其是在处理微生物组数据中的相对丰度数据时非常有用。该插件可以帮助用户探索和比较微生物组中微生物群落的组成。
qiime composition --help
Usage: qiime composition [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports methods for compositional data
analysis.
Plugin website: https://github.com/qiime2/q2-composition
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
add-pseudocount Add pseudocount to table.
ancom Apply ANCOM to identify features that differ in abundance.
ancombc Analysis of Composition of Microbiomes with Bias Correction
da-barplot Differential abundance bar plots
tabulate View tabular output from ANCOM-BC.
# 导入数据
qiime composition add-pseudocount \
--i-table table.qza \
--o-composition-table composition.qza
#数据转换
qiime composition ilr-transform \
--i-table composition.qza \
--o-transformed-table ilr_composition.qza
#可视化分析结果
qiime composition pcoa \
--i-table ilr_composition.qza \
--o-pcoa ilr_composition_pcoa.qza
qiime emperor plot \
--i-pcoa ilr_composition_pcoa.qza \
--m-metadata-file metadata.txt \
--o-visualization ilr_composition_emperor.qzv
q2-cutadapt
q2-cutadapt插件是用于对DNA序列数据进行预处理和过滤的工具。它基于Cutadapt软件,允许用户对Illumina测序数据进行裁剪(trimming)、过滤(filtering)和修剪(adapter removal)等操作,以消除低质量序列、去除适配器、修剪序列末端等。这有助于提高序列数据的质量,为后续的分析准备干净、高质量的数据。
#
qiime cutadapt --help
Usage: qiime cutadapt [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin uses cutadapt to work with adapters (e.g.
barcodes, primers) in sequence data.
Plugin website: https://github.com/qiime2/q2-cutadapt
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
demux-paired Demultiplex paired-end sequence data with barcodes in-
sequence.
demux-single Demultiplex single-end sequence data with barcodes in-
sequence.
trim-paired Find and remove adapters in demultiplexed paired-end
sequences.
trim-single Find and remove adapters in demultiplexed single-end
sequences.
qiime cutadapt trim-paired \
--i-demultiplexed-sequences demux.qza \
--p-cores 8 \
--p-front-f CCTACGGGNGGCWGCAG \
--p-front-r GACTACHVGGGTATCTAATCC \
--p-discard-untrimmed \
--o-trimmed-sequences demux_trimmed.qza
参数解释:
–i-demultiplexed-sequences: 输入的序列文件(需提前导入到QIIME 2)。
–p-cores: 并行处理的CPU核心数量。
–p-front-f 和 --p-front-r: 正向和反向引物序列。
–p-discard-untrimmed: 丢弃未被修剪的序列。
–o-trimmed-sequences: 输出修剪后的序列文件。
q2-dada2是QIIME 2的插件之一,基于DADA2算法,用于去噪和分析Illumina测序生成的16S rRNA数据。
qiime dada2 --help
Usage: qiime dada2 [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin wraps DADA2 and supports sequence quality
control for single-end and paired-end reads using the DADA2 R library.
Plugin website: http://benjjneb.github.io/dada2/
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
denoise-ccs Denoise and dereplicate single-end Pacbio CCS
denoise-paired Denoise and dereplicate paired-end sequences
denoise-pyro Denoise and dereplicate single-end pyrosequences
denoise-single Denoise and dereplicate single-end sequences
qiime dada2 denoise-single \
--i-demultiplexed-seqs input-demux.qza \
--p-trim-left 0 \
--p-trunc-len 120 \
--o-representative-sequences rep-seqs-dada2.qza \
--o-table table-dada2.qza \
--o-denoising-stats stats-dada2.qza
参数说明:
-
--i-demultiplexed-seqs
:输入的demultiplexed序列文件。 -
--p-trim-left
:要去除的序列的前部分碱基数量。 -
--p-trunc-len
:截断序列的长度。 -
--o-representative-sequences
:输出的代表序列文件。 -
--o-table
:生成的特征表文件。 -
--o-denoising-stats
:生成的去噪统计文件。 -
q2-deblur
q2-deblur插件通过识别和去除16S rRNA基因测序数据中的测序错误和噪声,以生成高质量的序列数据。其主要步骤包括:
- 生成特征表(Feature table): 从原始的FASTQ格式文件中导入数据,创建特征表。
- 质量过滤: 过滤低质量序列,去除低质量序列读数。
- 去噪处理: 使用Deblur算法去除测序错误和噪声,生成高质量的特征序列。
- 生成结果: 输出一个经过去噪处理和质量过滤的特征表和序列文件。
qiime deblur --help
Usage: qiime deblur [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin wraps the Deblur software for performing
sequence quality control.
Plugin website: https://github.com/biocore/deblur
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
denoise-16S Deblur sequences using a 16S positive filter.
denoise-other Deblur sequences using a user-specified positive filter.
visualize-stats Visualize Deblur stats per sample.
qiime deblur denoise-16S \
--i-demultiplexed-seqs your_qza_file.qza \
--p-trim-length 250 \ # 设置序列截断长度
--o-representative-sequences rep_seqs.qza \
--o-table table.qza \
--p-sample-stats \ # 如果需要生成样本统计信息
--o-stats deblur_stats.qza
结果数据导出
# 结果数据导出
qiime tools export --input-path rep_seqs.qza --output-path exported_rep_seqs
qiime tools export --input-path table.qza --output-path exported_table
qiime tools export --input-path deblur_stats.qza --output-path exported_stats
q2-demux 插件用于处理 DNA 或 RNA 测序数据的样本数据解复用(demultiplexing)和质量控制。这个插件允许用户根据样本的不同 DNA 或 RNA 序列标签(barcode 或者 Illumina 测序的 index)将混合测序数据集拆分成单独的样本。下面是 q2-demux 插件的基本介绍和使用步骤:
q2-demux 插件功能:
-
数据解复用(Demultiplexing):
- 将混合测序数据根据每个样本的唯一标识(barcode 或 index)分割成单独的样本序列文件。
-
质量控制:
- 提供了检查序列数据质量的功能,允许用户查看样本数据的质量分数并进行必要的处理,比如修剪或过滤低质量序列。
qiime demux --help
Usage: qiime demux [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports demultiplexing of single-end and
paired-end sequence reads and visualization of sequence quality information.
Plugin website: https://github.com/qiime2/q2-demux
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
emp-paired Demultiplex paired-end sequence data generated
with the EMP protocol.
emp-single Demultiplex sequence data generated with the EMP
protocol.
filter-samples Filter samples out of demultiplexed data.
partition-samples-paired Split demultiplexed sequence data into partitions.
partition-samples-single Split demultiplexed sequence data into partitions.
subsample-paired Subsample paired-end sequences without
replacement.
subsample-single Subsample single-end sequences without
replacement.
summarize Summarize counts per sample.
tabulate-read-counts Tabulate counts per sample
# 执行去重复
qiime demux emp-paired \
--i-seqs demux.qza \
--m-barcodes-file sample-metadata.tsv \
--m-barcodes-column BarcodeSequence \
--o-per-sample-sequences demux-paired-end.qza \
--o-error-correction-details demux-details.qza
## 查看结果
qiime demux summarize \
--i-data demux-paired-end.qza \
--o-visualization demux-summary.qzv
q2-diversity
是其中一个用于计算和分析生物多样性的插件。它可以帮助你评估样本群落的多样性和差异性。
qiime diversity --help
Usage: qiime diversity [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports metrics for calculating and
exploring community alpha and beta diversity through statistics and
visualizations in the context of sample metadata.
Plugin website: https://github.com/qiime2/q2-diversity
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
adonis adonis PERMANOVA test for beta group significance
alpha Alpha diversity
alpha-correlation Alpha diversity correlation
alpha-group-significance Alpha diversity comparisons
alpha-phylogenetic Alpha diversity (phylogenetic)
alpha-rarefaction Alpha rarefaction curves
beta Beta diversity
beta-correlation Beta diversity correlation
beta-group-significance Beta diversity group significance
beta-phylogenetic Beta diversity (phylogenetic)
beta-rarefaction Beta diversity rarefaction
bioenv bioenv
core-metrics Core diversity metrics (non-phylogenetic)
core-metrics-phylogenetic Core diversity metrics (phylogenetic and non-
phylogenetic)
filter-distance-matrix Filter samples from a distance matrix.
mantel Apply the Mantel test to two distance matrices
partial-procrustes Partial Procrustes
pcoa Principal Coordinate Analysis
pcoa-biplot Principal Coordinate Analysis Biplot
procrustes-analysis Procrustes Analysis
tsne t-distributed stochastic neighbor embedding
umap Uniform Manifold Approximation and Projection
# Alpha多样性(样本内部多样性)
# 计算Shannon指数:
qiime diversity alpha \
--i-table your_feature_table.qza \
--p-metric shannon \
--o-alpha-diversity shannon_vector.qza
#Beta多样性(样本间多样性)
# 计算Bray-Curtis距离:
qiime diversity beta \
--i-table your_feature_table.qza \
--p-metric braycurtis \
--o-distance-matrix braycurtis_distance_matrix.qza
# 可视化和统计分析
qiime diversity alpha-group-significance \
--i-alpha-diversity shannon_vector.qza \
--m-metadata-file your_sample_metadata.txt \
--o-visualization shannon_group_significance.qzv
qiime diversity beta-group-significance \
--i-distance-matrix braycurtis_distance_matrix.qza \
--m-metadata-file your_sample_metadata.txt \
--o-visualization braycurtis_group_significance.qzv
q2-diversity-lib 简介
q2-diversity-lib是QIIME 2的一个插件,用于计算多样性指数和样本间的差异。它基于多种生物多样性指标来评估微生物群落的多样性,并允许用户进行统计比较和可视化。
功能特性
- 计算多样性指数:支持计算多种多样性指数,如Shannon、Simpson、Chao1等,可以帮助衡量群落内物种的多样性和丰富度。
- Beta多样性计算:计算不同样本之间的差异和相似性,例如Bray-Curtis、Jaccard、Unweighted UniFrac、Weighted UniFrac等距离指标。
- Beta多样性可视化:生成多样性分析的可视化图表,如PCoA(Principal Coordinates Analysis)图表,展示样本之间的差异。
- 组间比较:支持组间多样性比较,通过PERMANOVA(Permutational Multivariate Analysis of Variance)等方法进行样本群落的差异性分析。
qiime diversity-lib --help
Usage: qiime diversity-lib [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin computes individual metrics for community
alpha and beta diversity.
Plugin website: https://github.com/qiime2/q2-diversity-lib
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
alpha-passthrough Alpha Passthrough (non-phylogenetic)
beta-passthrough Beta Passthrough (non-phylogenetic)
beta-phylogenetic-meta-passthrough
Beta Phylogenetic Meta Passthrough
beta-phylogenetic-passthrough Beta Phylogenetic Passthrough
bray-curtis Bray-Curtis Dissimilarity
faith-pd Faith's Phylogenetic Diversity
jaccard Jaccard Distance
observed-features Observed Features
pielou-evenness Pielou's Evenness
shannon-entropy Shannon's Entropy
unweighted-unifrac Unweighted Unifrac
weighted-unifrac Weighted Unifrac
计算使用
#计算Alpha多样性(多样性指数)
qiime diversity alpha \
--i-table table.qza \
--p-metric shannon \
--o-alpha-diversity shannon_alpha.qza
#计算Beta多样性距离
qiime diversity beta \
--i-table table.qza \
--p-metric braycurtis \
--o-distance-matrix braycurtis_distance.qza
#可视化Beta多样性分析结果(例如PCoA)
qiime diversity pcoa \
--i-distance-matrix braycurtis_distance.qza \
--o-pcoa braycurtis_pcoa.qza
qiime emperor plot \
--i-pcoa braycurtis_pcoa.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization braycurtis_emperor.qzv
#进行组间多样性比较(以PERMANOVA为例)
qiime diversity beta-group-significance \
--i-distance-matrix braycurtis_distance.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization braycurtis_permanova.qzv \
--p-method permanova
qiime emperor --help
Usage: qiime emperor [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin wraps Emperor and supports interactive
visualization of ordination plots.
Plugin website: http://emperor.microbio.me
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
biplot Visualize and Interact with Principal Coordinates Analysis
Biplot
plot Visualize and Interact with Principal Coordinates Analysis
Plots
procrustes-plot Visualize and Interact with a procrustes plot
q2-feature-classifier 是 QIIME 2 中的一个插件,用于对16S rRNA或ITS等序列数据进行分类和注释。它主要用于将序列分类为特定的分类单元,比如对OTUs(操作分类单元)或者物种进行分类。
qiime feature-classifier --help
Usage: qiime feature-classifier [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports taxonomic classification of
features using a variety of methods, including Naive Bayes, vsearch, and
BLAST+.
Plugin website: https://github.com/qiime2/q2-feature-classifier
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
blast BLAST+ local alignment search.
classify-consensus-blast BLAST+ consensus taxonomy classifier
classify-consensus-vsearch VSEARCH-based consensus taxonomy classifier
classify-hybrid-vsearch-sklearn
ALPHA Hybrid classifier: VSEARCH exact match
+ sklearn classifier
classify-sklearn Pre-fitted sklearn-based taxonomy classifier
extract-reads Extract reads from reference sequences.
find-consensus-annotation Find consensus among multiple annotations.
fit-classifier-naive-bayes Train the naive_bayes classifier
fit-classifier-sklearn Train an almost arbitrary scikit-learn
classifier
makeblastdb Make BLAST database.
vsearch-global VSEARCH global alignment search
#训练一个 SILVA 数据库上的分类器可以使用如下命令
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads silva-132-99-515-806-nb-classifier.qza \
--i-reference-taxonomy silva-132-99-515-806-nb-classifier.qza \
--o-classifier classifier.qza
# 使用训练好的分类器对样本数据进行分类
qiime feature-classifier classify-sklearn \
--i-classifier classifier.qza \
--i-reads paired-end-demux.qza \
--o-classification taxonomy.qza
q2-feature-table
插件是 QIIME 2 中的一个重要插件,用于处理和操作特征表(feature table)数据,它包括了许多功能,用于对微生物组数据进行分析和可视化。
以下是 q2-feature-table
插件的一些主要功能和使用方法:
- 导入特征表数据: 可以使用该插件将不同格式的特征表数据导入到 QIIME 2 中,如BIOM格式、文本格式、或其他常见格式的特征表。
- 特征表汇总和统计: 可以对特征表进行汇总和统计描述,比如计算每个样本中的特征数量、每个特征在样本中的出现频率等。
- 特征表的过滤和修剪: 提供了多种方法对特征表进行过滤和修剪,如去除低频特征、去除低丰度特征、保留指定样本数或特征数等。
- 特征表的转换和变换: 可以对特征表进行转换,如转置、归一化、对数转换等,以适应不同类型的分析需求。
- 特征表的合并和拆分: 可以将多个特征表合并为一个,也可以根据样本元数据信息将特征表拆分为多个子集。
- 特征表的可视化: 支持对特征表进行可视化展示,比如生成特征数量分布图、绘制热图展示特征在样本中的丰度等。
qiime feature-table --help
Usage: qiime feature-table [OPTIONS] COMMAND [ARGS]...
Description: This is a QIIME 2 plugin supporting operations on sample by
feature tables, such as filtering, merging, and transforming tables.
Plugin website: https://github.com/qiime2/q2-feature-table
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
core-features Identify core features in table
filter-features Filter features from table
filter-features-conditionally Filter features from a table based on
abundance and prevalence
filter-samples Filter samples from table
filter-seqs Filter features from sequences
group Group samples or features by a metadata
column
heatmap Generate a heatmap representation of a
feature table
merge Combine multiple tables
merge-seqs Combine collections of feature sequences
merge-taxa Combine collections of feature taxonomies
presence-absence Convert to presence/absence
rarefy Rarefy table
relative-frequency Convert to relative frequencies
rename-ids Renames sample or feature ids in a table
split Split one feature table into many
subsample Subsample table
summarize Summarize table
tabulate-seqs View sequence associated with each feature
transpose Transpose a feature table.
#特征表的摘要和统计信息
qiime feature-table summarize \
--i-table feature-table.qza \
--o-visualization feature-table-summary.qzv
#特征表的过滤和修剪
qiime feature-table filter-features \
--i-table feature-table.qza \
--p-min-frequency 10 \
--o-filtered-table filtered-feature-table.qza
qiime feature-table filter-samples \
--i-table feature-table.qza \
--p-min-frequency 500 \
--o-filtered-table filtered-sample-table.qza
# 特征表的合并和操作
qiime feature-table merge \
--i-tables table1.qza \
--i-tables table2.qza \
--o-merged-table merged-table.qza
#计算特征表的β-diversity:
qiime diversity beta \
--i-table feature-table.qza \
--o-distance-matrix beta-diversity.qza \
--p-metric braycurtis
#可视化特征表
qiime feature-table summarize \
--i-table feature-table.qza \
--o-visualization feature-table-summary.qzv
#可视化β-diversity距离矩阵
qiime diversity beta-phylogenetic \
--i-table feature-table.qza \
--i-phylogeny rooted-tree.qza \
--o-distance-matrix beta-diversity.qza \
--p-metric unweighted_unifrac
qiime diversity pcoa \
--i-distance-matrix beta-diversity.qza \
--o-pcoa pcoa-results.qza
qiime emperor plot \
--i-pcoa pcoa-results.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization emperor.qzv
q2-fragment-insertion插件是用于将未分配的DNA序列(通常是16S rRNA或18S rRNA序列)嵌入(插入)到预先构建的参考进化树中的工具。这个插件可以帮助解决一些问题,比如通过将未知序列嵌入到进化树中,来推断未知序列的系统发育位置。
qiime fragment-insertion --help
Usage: qiime fragment-insertion [OPTIONS] COMMAND [ARGS]...
Description: No description available. See plugin website:
https://github.com/qiime2/q2-fragment-insertion
Plugin website: https://github.com/qiime2/q2-fragment-insertion
Getting user support: https://github.com/qiime2/q2-fragment-insertion/issues
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
classify-otus-experimental Experimental: Obtain taxonomic lineages, by
finding closest OTU in reference phylogeny.
filter-features Filter fragments in tree from table.
sepp Insert fragment sequences using SEPP into
reference phylogenies.
qiime fragment-insertion sepp \
--i-representative-sequences <代表序列文件.qza> \
--i-reference-database <参考数据库.qza> \
--o-tree <输出进化树.qza> \
--o-placements <输出插入位置文件.qza>
-
--i-representative-sequences
是代表性序列文件的位置。 -
--i-reference-database
是参考数据库文件的位置。 -
--o-tree
指定输出的进化树文件。 -
--o-placements
指定输出的插入位置文件。 -
q2-longitudinal
q2-longitudinal 插件是 QIIME 2 中的一个插件,专门用于处理微生物组长期研究的数据。该插件允许用户对时间序列实验数据进行分析,以便检测微生物组随时间变化的情况,比较不同条件下的变化,以及对这些变化的统计显著性进行评估。
以下是 q2-longitudinal 插件的一些主要功能和使用命令:
主要功能:
- 时间序列数据可视化:生成时间序列样本数据的可视化图表,比如长期研究的变化趋势、样本之间的差异等。
- 差异分析:比较不同时间点或不同处理组之间的微生物组成差异。
- Alpha 和 Beta 多样性分析:评估微生物群落在时间序列中的多样性和相似性变化。
- 线性混合效应模型:对微生物组数据进行线性模型分析,以研究时间、处理效应和其交互作用对微生物组成的影响。
qiime longitudinal --help
Usage: qiime longitudinal [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports methods for analysis of time
series data, involving either paired sample comparisons or longitudinal
study designs.
Plugin website: https://github.com/qiime2/q2-longitudinal
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
anova ANOVA test
feature-volatility Feature volatility analysis
first-differences Compute first differences or difference from
baseline between sequential states
first-distances Compute first distances or distance from baseline
between sequential states
linear-mixed-effects Linear mixed effects modeling
maturity-index Microbial maturity index prediction.
nmit Nonparametric microbial interdependence test
pairwise-differences Paired difference testing and boxplots
pairwise-distances Paired pairwise distance testing and boxplots
plot-feature-volatility Plot longitudinal feature volatility and
importances
volatility Generate interactive volatility plot
#导入数据
qiime longitudinal feature-table-merge \
--i-longitudinal-feature-tables feature-table.qza \
--o-merged-table merged-table.qza
#线性混合效应模型
qiime longitudinal linear-mixed-effects \
--m-metadata-file sample-metadata.tsv \
--m-metadata-file timepoints.tsv \
--p-metric Shannon_index \
--p-group-columns treatment \
--p-state-column time \
--p-individual-id-column subject \
--o-visualization lme-results.qzv
#可视化
qiime longitudinal volatility \
--i-table merged-table.qza \
--m-metadata-file sample-metadata.tsv \
--p-state-column time \
--p-individual-id-column subject \
--o-visualization volatility.qzv
#组间差异
qiime longitudinal pairwise-differences \
--m-metadata-file sample-metadata.tsv \
--m-metadata-file timepoints.tsv \
--p-metric Shannon_index \
--p-group-column treatment \
--p-state-column time \
--p-individual-id-column subject \
--o-visualization pairwise-differences.qzv
#α多样性图表
qiime longitudinal maturity-index \
--i-alpha-diversity alpha-diversity.qza \
--m-metadata-file sample-metadata.tsv \
--p-state-column time \
--p-individual-id-column subject \
--o-visualization maturity-index.qzv
q2-metadata 插件用于处理和操作元数据,元数据是描述样本信息的数据,比如样本来源、处理方法、实验条件等。以下是 q2-metadata 插件的简要介绍和一些常见的使用命令:
q2-metadata 插件的功能:
- 元数据导入: 将元数据文件导入到 QIIME 2 格式中。
- 元数据可视化: 可视化元数据内容以便更好地理解样本信息。
- 元数据的处理和编辑: 对元数据进行筛选、编辑和转换。
- 元数据统计和摘要: 统计和生成关于元数据的摘要信息。
qiime metadata --help
Usage: qiime metadata [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin provides functionality for working with and
visualizing Metadata.
Plugin website: https://github.com/qiime2/q2-metadata
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
distance-matrix Create a distance matrix from a numeric Metadata column
merge Merge metadata
shuffle-groups Shuffle values in a categorical sample metadata column.
tabulate Interactively explore Metadata in an HTML table
# 1. 元数据导入:
qiime metadata tabulate --m-input-file sample-metadata.tsv --o-visualization sample-metadata.qzv
# 2. 元数据可视化:
qiime metadata tabulate --m-input-file sample-metadata.qza --o-visualization sample-metadata.qzv
# 3. 元数据编辑与处理:
# 删除列:
qiime metadata tabulate --m-input-file sample-metadata.qza --o-visualization sample-metadata.qzv
# 筛选行(过滤):
qiime metadata tabulate --m-input-file sample-metadata.qza --o-visualization sample-metadata.qzv
# 4. 元数据统计和摘要:
qiime metadata tabulate --m-input-file sample-metadata.qza --o-visualization sample-me
q2-phylogeny插件则提供了处理生物多样性分析中的系统发育信息的功能。该插件主要用于构建系统发育树和处理系统发育树相关的操作,例如序列的进化树推断、进化树的根节点分配等。
qiime phylogeny --help
Usage: qiime phylogeny [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports generating and manipulating
phylogenetic trees.
Plugin website: https://github.com/qiime2/q2-phylogeny
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
align-to-tree-mafft-fasttree Build a phylogenetic tree using fasttree and
mafft alignment
align-to-tree-mafft-iqtree Build a phylogenetic tree using iqtree and
mafft alignment.
align-to-tree-mafft-raxml Build a phylogenetic tree using raxml and
mafft alignment.
fasttree Construct a phylogenetic tree with FastTree.
filter-table Remove features from table if they're not
present in tree.
filter-tree Remove features from tree based on metadata
iqtree Construct a phylogenetic tree with IQ-TREE.
iqtree-ultrafast-bootstrap Construct a phylogenetic tree with IQ-TREE
with bootstrap supports.
midpoint-root Midpoint root an unrooted phylogenetic tree.
raxml Construct a phylogenetic tree with RAxML.
raxml-rapid-bootstrap Construct a phylogenetic tree with bootstrap
supports using RAxML.
robinson-foulds Calculate Robinson-Foulds distance between
phylogenetic trees.
## 构建系统发育树:
#使用多序列比对后的结果构建系统发育树。可以使用q2-phylogeny中的FastTree或RAxML进行树的构建。以下是使用FastTree的示例命令:
qiime phylogeny fasttree \
--i-alignment aligned-sequences.qza \
--o-tree tree.qza
# 或者使用RAxML进行系统发育树的构建:
qiime phylogeny raxml \
--i-alignment aligned-sequences.qza \
--p-substitution-model GTRGAMMA \
--o-tree tree.qza \
--verbose
## 可选操作 - 根节点分配:
# 有时,你可能需要为系统发育树分配根节点。可以使用q2-phylogeny中的根节点分配插件进行此操作。以下是一个示例命令:
qiime phylogeny midpoint-root \
--i-tree tree.qza \
--o-rooted-tree rooted-tree.qza
q2-quality-control 插件旨在进行序列数据的质量控制和过滤,它可以执行以下任务:
q2-quality-filter
插件用于对DNA测序数据进行质量控制和过滤,以去除低质量的序列。这有助于提高后续分析的准确性和可靠性。
qiime quality-control --help
Usage: qiime quality-control [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports methods for assessing and
controlling the quality of feature and sequence data.
Plugin website: https://github.com/qiime2/q2-quality-control
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
bowtie2-build Build bowtie2 index from reference sequences.
decontam-identify Identify contaminants
decontam-identify-batches Identify contaminants in Batch Mode
decontam-remove Removes contaminant
decontam-score-viz Generate a histogram representation of the scores
evaluate-composition Evaluate expected vs. observed taxonomic
composition of samples
evaluate-seqs Compare query (observed) vs. reference (expected)
sequences.
evaluate-taxonomy Evaluate expected vs. observed taxonomic
assignments
exclude-seqs Exclude sequences by alignment
filter-reads Filter demultiplexed sequences by alignment to
reference database.
qiime quality-filter q-score \
--i-demux paired-end-demux.qza \
--p-min-quality 20 \
--o-filtered-sequences demux-filtered.qza \
--o-filter-stats demux-filter-stats.qza
而q2-sample-classifier是Qiime 2中的一个插件,用于样本分类和预测。它可以帮助用户利用机器学习算法对样本进行分类,比较不同条件下的微生物组成差异,例如,预测分类数据(如临床数据)和微生物组成之间的关系。
qiime sample-classifier --help
Usage: qiime sample-classifier [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin supports methods for supervised
classification and regression of sample metadata, and other supervised
machine learning methods.
Plugin website: https://github.com/qiime2/q2-sample-classifier
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--example-data PATH Write example data and exit.
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[外链图片转存中...(img-vEaBGJ99-1714367457740)]
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* **200道Linux面试题**
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* **174道运维工程师面试题**
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> 2、在工作中,运维人员经常需要跟运营人员打交道,请问运营人员是做什么工作的?
> 3、现在给你三百台服务器,你怎么对他们进行管理?
> 4、简述raid0 raid1raid5二种工作模式的工作原理及特点
> 5、LVS、Nginx、HAproxy有什么区别?工作中你怎么选择?
> 6、Squid、Varinsh和Nginx有什么区别,工作中你怎么选择?
> 7、Tomcat和Resin有什么区别,工作中你怎么选择?
> 8、什么是中间件?什么是jdk?
> 9、讲述一下Tomcat8005、8009、8080三个端口的含义?
> 10、什么叫CDN?
> 11、什么叫网站灰度发布?
> 12、简述DNS进行域名解析的过程?
> 13、RabbitMQ是什么东西?
> 14、讲一下Keepalived的工作原理?
> 15、讲述一下LVS三种模式的工作过程?
> 16、mysql的innodb如何定位锁问题,mysql如何减少主从复制延迟?
> 17、如何重置mysql root密码?
**网上学习资料一大堆,但如果学到的知识不成体系,遇到问题时只是浅尝辄止,不再深入研究,那么很难做到真正的技术提升。**
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