How to construct qiime2 Classifier
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Construction of qiime2 18s Classifier
# # wget-c https://www.arb-silva.de/fileadmin/silva_databases/qiime/SILVA_132_QIIME_release.zip####unzip SILVA_132_QIIME_release.zipqiime 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.qzaqiime 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# length filtering 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# repeat sequences merge 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# full-length classifier to build 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/ 39qiime 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.qzaqiime 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.qzaqiime 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 read here This article "how to build qiime2 classifiers" has been introduced, and if you want to master the knowledge points of this article, you still need to practice and use it. If you want to know more about the article, please follow the industry information channel.
