https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494
利用工具建立数据库 rescript
qiime rescript get-silva-data \
--p-version '138' \
--p-target 'SSURef_NR99' \
--p-include-species-labels \
--o-silva-sequences silva-138-ssu-nr99-seqs.qza \
--o-silva-taxonomy silva-138-ssu-nr99-tax.qza
这个代码自动获取 99相似性的序列和分类信息，由于网络原因一般运行报错
可以直接下载qiime2官方网站i提供的文件：https://docs.qiime2.org/2020.8/data-resources/
wget -c https://data.qiime2.org/2020.8/common/silva-138-99-seqs.qza
wget -c https://data.qiime2.org/2020.8/common/silva-138-99-tax.qza
ln -s silva-138-99-tax.qza silva-138-ssu-nr99-tax.qza
ln -s silva-138-99-seqs.qza silva-138-ssu-nr99-seqs.qza
之后就可以参考这里建立自己的分类器：https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494
#remove sequences that contain 5 or more ambiguous bases (IUPAC compliant ambiguity bases) and any homopolymers that are 8 or more bases in length
qiime rescript cull-seqs \
--i-sequences silva-138-ssu-nr99-seqs.qza \
--o-clean-sequences silva-138-ssu-nr99-seqs-cleaned.qza
#长度过滤
qiime rescript filter-seqs-length-by-taxon \
--i-sequences silva-138-ssu-nr99-seqs-cleaned.qza \
--i-taxonomy silva-138-ssu-nr99-tax.qza \
--p-labels Archaea Bacteria Eukaryota \
--p-min-lens 900 1200 1400 \
--o-filtered-seqs silva-138-ssu-nr99-seqs-filt.qza \
--o-discarded-seqs silva-138-ssu-nr99-seqs-discard.qza
#重复序列合并
qiime rescript dereplicate \
--i-sequences silva-138-ssu-nr99-seqs-filt.qza \
--i-taxa silva-138-ssu-nr99-tax.qza \
--p-rank-handles 'silva' \
--p-mode 'uniq' \
--o-dereplicated-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \
--o-dereplicated-taxa silva-138-ssu-nr99-tax-derep-uniq.qza
#全长分类器构建
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads silva-138-ssu-nr99-seqs-derep-uniq.qza \
--i-reference-taxonomy silva-138-ssu-nr99-tax-derep-uniq.qza \
--o-classifier silva-138-ssu-nr99-classifier.qza
##特异引物分类器构建1
#截取序列
qiime feature-classifier extract-reads \
--i-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \
--p-f-primer GTGYCAGCMGCCGCGGTAA \
--p-r-primer GGACTACNVGGGTWTCTAAT \
--p-n-jobs 2 \
--p-read-orientation 'forward' \
--o-reads silva-138-ssu-nr99-seqs-515f-806r.qza
#合并重复
qiime rescript dereplicate \
--i-sequences silva-138-ssu-nr99-seqs-515f-806r.qza \
--i-taxa silva-138-ssu-nr99-tax-derep-uniq.qza \
--p-rank-handles 'silva' \
--p-mode 'uniq' \
--o-dereplicated-sequences silva-138-ssu-nr99-seqs-515f-806r-uniq.qza \
--o-dereplicated-taxa silva-138-ssu-nr99-tax-515f-806r-derep-uniq.qza
#构建分类器
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads silva-138-ssu-nr99-seqs-515f-806r-uniq.qza \
--i-reference-taxonomy silva-138-ssu-nr99-tax-515f-806r-derep-uniq.qza \
--o-classifier silva-138-ssu-nr99-515f-806r-classifier.qza
##特异引物分类器构建2
# 338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and. 806R (5′-GGACTACHVGGGTWTCTAAT-3′)
#截取序列
qiime feature-classifier extract-reads \
--i-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \
--p-f-primer ACTCCTACGGGAGGCAGCAG \
--p-r-primer GGACTACHVGGGTWTCTAAT \
--p-n-jobs 2 \
--p-read-orientation 'forward' \
--o-reads silva-138-ssu-nr99-seqs-338f-806r.qza
#合并重复
qiime rescript dereplicate \
--i-sequences silva-138-ssu-nr99-seqs-338f-806r.qza \
--i-taxa silva-138-ssu-nr99-tax-derep-uniq.qza \
--p-rank-handles 'silva' \
--p-mode 'uniq' \
--o-dereplicated-sequences silva-138-ssu-nr99-seqs-338f-806r-uniq.qza \
--o-dereplicated-taxa silva-138-ssu-nr99-tax-338f-806r-derep-uniq.qza
#构建分类器
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads silva-138-ssu-nr99-seqs-338f-806r-uniq.qza \
--i-reference-taxonomy silva-138-ssu-nr99-tax-338f-806r-derep-uniq.qza \
--o-classifier silva-138-ssu-nr99-338f-806r-classifier.qza
注意：qiime2建立分类数据库很消耗内存，至少50G以上；这里我建立好的数据库分享给大家：
链接：https://pan.baidu.com/s/11FRnvS_-qzPCFF5FKRmJGw
提取码：g3yr
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