Q2GreengenesDiversity
Computing various diversity index and taxonomy assessement of ASVs using GreenGenes
Qiime2TaxonomyDiversityExtractor 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 GreenGenes (in version 13.8) with reference full-length sequences clustered at 99% sequence similarity.
Minimum required configuration: Digital lab SC2
About GreenGenes:
The GreenGenes database is no longer being maintained. The last version is version 13.8 (2013). We suggest to use the task Qiime2 RDP & diversity or Qiime2 NCBI & diversity or Qiime2 Silva & diversity instead.
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
stringGreenGenes-v13.8 GreenGenes-v13.8threads
Number of threads
int2