Kraken2 Vs qiime2 16S物种注释

# 激活环境
source  ~/miniconda3/bin/activate
conda activate kraken2
# 下载数据库
wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/16S_Greengenes13.5_20200326.tgz
# 解压
 tar zxvf 16S_Greengenes13.5_20200326.tgz
# 物种分类
DBNAME=16S_Greengenes_k2db/
SAMPLE="s5630696"
THREADS=8

kraken2 \
--db ${DBNAME} \
--threads ${THREADS} \
--report ${SAMPLE}.kreport2 \
--paired ${SAMPLE}_1.fastq ${SAMPLE}_2.fastq > ${SAMPLE}.kraken2

# 获得相对丰度
bracken -d ${DBNAME} -r 150 -l G -i ${SAMPLE}.kreport2 -o ${SAMPLE}_g.bracken

# 这里只从物种注释开始，前面的见官方文档或者宏基因组公众号的中文翻译
qiime feature-classifier classify-sklearn
--i-classifier classifier_gg13_8.qza
-i-reads rep_seqs_${SAMPLE}.qza
--o-classification ${SAMPLE}_classsified_gg.qza
--verbose
--p-n-jobs ${THREADS}
# 导出门和属的结果
for i in 2 6 
do 
qiime taxa collapse \
  --i-table table_final.qza \
  --i-taxonomy taxonomy.qza \
  --p-level $i \
  --o-collapsed-table table-l$i.qza
done

#导出 tsv
for file in ./table-l*.qza
do
  base=$(basename $file .qza)
  echo $base
  qiime tools export \
  --input-path $file \
  --output-path $base
  biom convert --to-tsv -i $base/feature-table.biom -o $base.tsv
done