silva-138_classifiers

V3 amplicons

Extracting V3 region

Primers: 341f & 518r

qiime feature-classifier extract-reads --i-sequences silva138_noEuk_AB_seqs_uniq.qza --p-f-primer CCTACGGGNGGCWGCAG --p-r-primer GTATTACCGCGGCTGCTGG --p-n-jobs 12 --o-reads silva138_AB_V3seqs.qza

Output: silva138_AB_V3seqs.qza

Dereplicating the target region

qiime rescript dereplicate --i-sequences silva138_AB_V3seqs.qza --i-taxa silva138_noEuk_AB_tax_uniq.qza --o-dereplicated-sequences silva138_AB_V3seqs_uniq.qza --o-dereplicated-taxa silva138_AB_V3taza_uniq.qza

Dereplicated Sequences: silva138_AB_V3seqs_uniq.qza
Dereplicated Taxa: silva138_AB_V3taxa_uniq.qza

Classifying & evaluating with RESCRIPt

Using multiple threads increases memory usage Ref. Using 1 thread with auto reads per batch (took approx 20 hrs)

qiime rescript evaluate-fit-classifier --i-sequences silva138_AB_V3seqs_uniq.qza --i-taxonomy silva138_AB_V3taxa_uniq.qza --o-classifier silva138_AB_V3_classifier.qza --o-observed-taxonomy silva138_AB_V3_predicted_taxonomy.qza --o-evaluation silva138_AB_V3_classifier_eval.qzv

Classifier: silva138_AB_V3_classifier.qza
Predicted Taxonomy: silva138_AB_V3_predicted_taxonomy.qza
Evaluation: silva138_AB_V3_classifier_eval.qzv

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