qiime2：安装与使用

试一下docker安装

docker pull quay.io/qiime2/amplicon:2024.10
docker images
docker run -v {挂载的目录}:/data quay.io/qiime2/amplicon:2024.10 qiime -h

使用

import.txt

docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path import.txt --output-path res/raw.qza --input-format SingleEndFastqManifestPhred33V2
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime demux summarize --i-data res/raw.qza --o-visualization res/raw.qzv
## dada2 ##
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime dada2 denoise-ccs --i-demultiplexed-seqs res/raw.qza --p-front AGRGTTTGATYNTGGCTCAG --p-adapter TASGGHTACCTTGTTASGACTT --p-min-len 1000  --p-max-len 1600 --p-n-threads 120 --o-table res/table.qza --o-representative-sequences res/seqs.qza --o-denoising-stats res/denoising-stats.qza
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime metadata tabulate --m-input-file res/denoising-stats.qza --o-visualization res/denoising-stats.qzv
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-table summarize --i-table res/table.qza --o-visualization res/table.qzv --m-sample-metadata-file metadata2.txt
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-table tabulate-seqs --i-data res/seqs.qza --o-visualization res/seqs.qzv
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools export --input-path  res/denoising-stats.qza --output-path res/denoising-stats
## Vsearch 99% clustering ##
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime vsearch cluster-features-open-reference --i-table res/table.qza --i-sequences res/seqs.qza --i-reference-sequences silva-138-99-seqs.qza --p-perc-identity 0.99 --p-threads 120 --o-clustered-table res/table99.qza --o-clustered-sequences res/seqs99.qza --o-new-reference-sequences res/newref99.qza
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-table summarize --i-table res/table99.qza --o-visualization res/table99.qzv --m-sample-metadata-file metadata2.txt
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-table tabulate-seqs --i-data res/seqs99.qza --o-visualization res/seqs99.qzv  
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-table tabulate-seqs --i-data res/newref99.qza --o-visualization res/newref99.qzv
## get features and sample tsv ##
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools export --input-path res/table99.qza --output-path res/table99.biom
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 biom convert -i res/table99.biom/feature-table.biom -o res/table99.tsv --to-tsv
##Taxonomy
#SILVA138
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 mkdir res/tax/
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads res/seqs99.qza --o-classification res/tax/taxonomy.qza
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime metadata tabulate --m-input-file res/tax/taxonomy.qza --o-visualization res/tax/taxonomy.qzv
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime taxa barplot --i-table res/table99.qza --i-taxonomy res/tax/taxonomy.qza --m-metadata-file metadata2.txt --o-visualization res/tax/taxa-bar-plots.qzv
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools export --input-path res/tax/taxonomy.qza --output-path res/tax/taxonomy
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools export --input-path res/tax/taxa-bar-plots.qzv --output-path res/tax/taxonomy_class1-6
#Greengenes2 2024.09
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 mkdir res/tax2/
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime feature-classifier classify-sklearn --i-classifier 2024.09.backbone.full-length.nb.sklearn-1.4.2.qza --i-reads res/seqs99.qza --o-classification res/tax2/taxonomy.qza
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime metadata tabulate --m-input-file res/tax2/taxonomy.qza --o-visualization res/tax2/taxonomy.qzv
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime taxa barplot --i-table res/table99.qza --i-taxonomy res/tax2/taxonomy.qza --m-metadata-file metadata2.txt --o-visualization res/tax2/taxa-bar-plots.qzv
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools export --input-path res/tax2/taxonomy.qza --output-path res/tax2/taxonomy
docker run -v ~/diarrhoea/MJ/qingzhu:/data quay.io/qiime2/amplicon:2024.10 qiime tools export --input-path res/tax2/taxa-bar-plots.qzv --output-path res/tax2/taxonomy_class1-6