物种分类鉴定及可视化
物种组成分析wget \-O "gg-13-8-99-515-806-nb-classifier.qza" \
"https://data.qiime2.org/2023.2/common/gg-13-8-99-515-806-nb-classifier.qza"
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime feature-classifier classify-sklearn \
--i-classifier gg-13-8-99-515-806-nb-classifier.qza \
--i-reads rep-seqs.qza \
--o-classification taxonomy.qza
#更换官网的注释库silva对比下结果
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime feature-classifier classify-sklearn \
--i-classifier silva-138-99-515-806-nb-classifier.qza \
--i-reads rep-seqs.qza \
--o-classification taxonomy_silva.qza
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime metadata tabulate \
--m-input-file taxonomy.qza \
--o-visualization taxonomy.qzv
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime metadata tabulate \
--m-input-file taxonomy_silva.qza \
--o-visualization taxonomy_silva.qzv
#下载到本地去view，结果相似。 物种分类完，画条形图
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime taxa barplot \
--i-table table.qza \
--i-taxonomy taxonomy.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization taxa-bar-plots.qzv
页:
[1]