怎么用qiime2分类器建立SILVA数据库

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.qzawget -c https://data.qiime2.org/2020.8/common/silva-138-99-tax.qzaln -s silva-138-99-tax.qza silva-138-ssu-nr99-tax.qzaln -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 lengthqiime 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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