qiime2 16s分析代码

由于16S分析涉及到多个步骤和工具，以下是一个基本的流程和代码示例。这个流程可以根据具体的研究目的和数据情况进行修改和调整。

1. 导入数据

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path manifest.csv \
  --output-path paired-end-demux.qza \
  --input-format PairedEndFastqManifestPhred33

2. 进行质量控制和过滤

qiime demux summarize \
  --i-data paired-end-demux.qza \
  --o-visualization paired-end-demux.qzv

qiime dada2 denoise-paired \
  --i-demultiplexed-seqs paired-end-demux.qza \
  --p-trim-left-f 0 \
  --p-trim-left-r 0 \
  --p-trunc-len-f 250 \
  --p-trunc-len-r 220 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza \
  --o-denoising-stats stats-dada2.qza

3. 对OTU进行注释

qiime feature-classifier classify-sklearn \
  --i-classifier classifier.qza \
  --i-reads rep-seqs-dada2.qza \
  --o-classification taxonomy.qza

qiime metadata tabulate \
  --m-input-file taxonomy.qza \
  --o-visualization taxonomy.qzv

4. 进行alpha和beta多样性分析

qiime diversity alpha-rarefaction \
  --i-table table-dada2.qza \
  --i-phylogeny rooted-tree.qza \
  --p-max-depth 10000 \
  --m-metadata-file mapping.txt \
  --o-visualization alpha-rarefaction.qzv

qiime diversity beta \
  --i-table table-dada2.qza \
  --p-metric braycurtis \
  --p-n-jobs -1 \
  --i-phylogeny rooted-tree.qza \
  --o-distance-matrix braycurtis-distance-matrix.qza

qiime diversity pcoa \
  --i-distance-matrix braycurtis-distance-matrix.qza \
  --o-pcoa braycurtis-pcoa.qza

qiime emperor plot \
  --i-pcoa braycurtis-pcoa.qza \
  --m-metadata-file mapping.txt \
  --p-custom-axes Treatment \
  --o-visualization emperor-braycurtis.qzv

5. 进行差异分析

qiime feature-table filter-samples \
  --i-table table-dada2.qza \
  --m-metadata-file metadata.tsv \
  --p-where "[Group]='Treatment1'" \
  --o-filtered-table table-treatment1.qza

qiime feature-table filter-samples \
  --i-table table-dada2.qza \
  --m-metadata-file metadata.tsv \
  --p-where "[Group]='Treatment2'" \
  --o-filtered-table table-treatment2.qza

qiime composition add-pseudocount \
  --i-table table-treatment1.qza \
  --o-composition-table comp-table-treatment1.qza

qiime composition add-pseudocount \
  --i-table table-treatment2.qza \
  --o-composition-table comp-table-treatment2.qza

qiime composition ancom \
  --i-table comp-table-treatment1.qza \
  --m-metadata-file metadata.tsv \
  --m-metadata-column Group \
  --o-visualization ancom-treatment1.qzv

qiime composition ancom \
  --i-table comp-table-treatment2.qza \
  --m-metadata-file metadata.tsv \
  --m-metadata-column Group \
  --o-visualization ancom-treatment2.qzv

以上是一个基本的16S分析流程和代码示例。根据具体的研究目的和数据情况，还可以添加其他步骤和工具进行分析。