本篇内容主要讲解“怎么用qiime2分类器建立SILVA数据库”，感兴趣的朋友不妨来看看。本文介绍的方法操作简单快捷，实用性强。下面就让小编来带大家学习“怎么用qiime2分类器建立SILVA数据库”吧!
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
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
#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
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