qiime2 18S 分类器构建：V 2020.8

##wget -c https://www.arb-silva.de/fileadmin/silva_databases/qiime/SILVA_132_QIIME_release.zip
####unzip SILVA_132_QIIME_release.zip
qiime tools import \
 --type 'FeatureData[Sequence]' \
 --input-path SILVA_132_QIIME_release/rep_set/rep_set_18S_only/99/silva_132_99_18S.fna \
 --output-path 18S_SILVA132_99_otus.qza
qiime tools import \
 --type 'FeatureData[Taxonomy]' \
 --input-format HeaderlessTSVTaxonomyFormat \
 --input-path SILVA_132_QIIME_release/taxonomy/18S_only/99/majority_taxonomy_all_levels.txt \
 --output-path 18S_SILVA132_99_taxonomy.qza

#长度过滤
qiime rescript filter-seqs-length-by-taxon \
    --i-sequences  18S_SILVA132_99_otus.qza \
    --i-taxonomy 18S_SILVA132_99_taxonomy.qza \
    --p-labels  Eukaryota \
    --p-min-lens  1400 \
    --o-filtered-seqs 18S_SILVA132_nr99-seqs-filt.qza \
    --o-discarded-seqs 18S_SILVA132_nr99-seqs-discard.qza
#重复序列合并
qiime rescript dereplicate \
    --i-sequences 18S_SILVA132_nr99-seqs-filt.qza  \
    --i-taxa 18S_SILVA132_99_taxonomy.qza \
    --p-rank-handles 'silva' \
    --p-mode 'uniq' \
    --o-dereplicated-sequences 18S_SILVA132-nr99-seqs-derep-uniq.qza \
    --o-dereplicated-taxa 18S_SILVA132-tax-derep-uniq.qza
#全长分类器构建
qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads  18S_SILVA132-nr99-seqs-derep-uniq.qza \
  --i-reference-taxonomy 18S_SILVA132-nr99-tax-derep-uniq.qza \
  --o-classifier 18S_SILVA132-nr99-classifier.qza

###http://www.earthmicrobiome.org/protocols-and-standards/18s/ 39
qiime feature-classifier extract-reads  \
   --i-sequences 18S_SILVA132_99_otus.qza \
 --p-f-primer GTACACACCGCCCGTC \
 --p-r-primer TGATCCTTCTGCAGGTTCACCTAC \
 --p-max-length 150 \
 --o-reads ref-seqs_18S_99_SILVA132_RL150.qza
qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads ref-seqs_18S_99_SILVA132_RL150.qza \
  --i-reference-taxonomy 18S_SILVA132_99_taxonomy.qza \
  --o-classifier 18S_EMB_SILVA132_classifier.qza
qiime feature-classifier fit-classifier-naive-bayes \
 --i-reference-reads 18S_SILVA132_99_otus.qza \
 --i-reference-taxonomy 18S_SILVA132_99_taxonomy.qza \
 --o-classifier 18S_full_SILVA132_classifier.qza

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