How to use qiime2 Classifier to build SILVA Database
This article mainly explains "how to use qiime2 classifier to establish SILVA database", interested friends may wish to take a look. The method introduced in this paper is simple, fast and practical. Let Xiaobian take you to learn "how to use qiime2 classifier to establish SILVA database"!
Using tools to establish database 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
This code automatically obtains 99 similarity sequences and classification information, and generally runs an error due to network reasons
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#length filterqiime 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#repeat sequence merge qiime rescript duplicate\ --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-deduplicated-taxa silva-138-ssu-nr99-tax-degenerate-uniq.qza#full-length classifier construction qiime feature-classifier fit-classifier-naive-bayes \ --i-reference-reads silva-138-ssu-nr99-seqs-degenerate-uniq. qza \ --i-reference-taxonomy silva-138-ssu-nr99-tax-degenerate-uniq.qza\ --o-classifier silva-138-ssu-nr 99-classifier.qza##specific primer classifier construction 1#intercept sequence 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#merge duplicate qiime rescript duplicate\ --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-deduplicated-taxa silva-138-ssu-nr99-tax-515f-806 r-deep-uniq.qza#build classifier qiime feature-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##specific primer classifier construct 2#338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and. 806R (5′-GGACTACHVGGGTWTCTAAT-3′)#intercept sequence 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#merge duplicate qiime rescript duplicate\ --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-deduplicated-taxa silva-138-ssu-nr99-tax-338f-806 r-deep-uniq.qza#build classifier qiime feature-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
Note: qiime2 to establish a classification database is very expensive memory, at least 50G above
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