Introduction Feature Frequency Table importer Feature Table importer Make metadata manifest Metagenome seq env task old_Q2FeatureInferenceSE Q2FeatureInferencePE Q2FeatureInferenceSE Q2GreengenesDiversity Q2NCBIDiversity Q2QualityCheck Q2RarefactionAnalysis Q2RDPDiversity Q2SilvaDiversity Qiime single-end sample frequencies Qiime1 env task Qiime2 ANCOM differential analysis Qiime2 env task Qiime2 feature frequencies (paired-end) Qiime2 manifest table exporter Qiime2 manifest table importer Qiime2 metadata table exporter Qiime2 metadata table importer Qiime2 metadata table maker Qiime2 rarefaction analysis Qiime2 taxa composition annotator Quality Table importer Rarefaction Table importer Taxonomy Table importer Taxonomy Table importer
Technical Documentation
Resources
Tasks
Q2SilvaDiversity
Computing various diversity index and taxonomy assessement of ASVs using Silva
Qiime2TaxonomyDiversitySilvaExtractor class.
This task classifies reads by taxon using a pre-fitted sklearn-based taxonomy classifier. By default, we suggest a pre-fitted Naive Bayes classifier for the database Silva (in version 13.8) with reference full-length sequences clustered at 99% sequence similarity.
Minimum required configuration: Digital lab SC2
About Silva: SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small Ribosomal RNA sequences.
Input
Output
Configuration
rarefaction_plateau_value
Depth of coverage when reaching the plateau of the curve on the previous step
inttaxonomic_affiliation_database
Database for taxonomic affiliation
stringSilva-v13.8 Silva-v13.8threads
Number of threads
int2