Learn to analyze microbiomes in QIIME: install software, set up environment, import data, visualize results, perform quality control, taxonomic analysis, diversity analysis.
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Install QIIME 2
Set Up Your Environment
conda activate qiime2-
.
qiime --help
. This should display the list of available commands, indicating a successful setup.
Import Your Data
.qza
artifact: qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path --output-path demux.qza
.
Visualize Raw Data
qiime demux summarize
to generate a visualization of your demultiplexed sequences: qiime demux summarize --i-data demux.qza --o-visualization demux.qzv
.
Quality Control and Feature Table Construction
qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 150 --o-representative-sequences rep-seqs.qza --o-table table.qza
.
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv
and for representative sequences: qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv
.
Taxonomic Analysis
qiime feature-classifier classify-sklearn --i-classifier --i-reads rep-seqs.qza --o-classification taxonomy.qza
.
qiime metadata tabulate --m-input-file taxonomy.qza --o-visualization taxonomy.qzv
.
Diversity Analysis
qiime diversity core-metrics-phylogenetic --i-phylogeny --i-table table.qza --p-sampling-depth --m-metadata-file --output-dir core-metrics-results
.
Export Data
qiime tools export --input-path table.qza --output-path exported-feature-table
.
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