Computing various diversity index and taxonomy assessement of ASVs using GreenGenes
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
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.
Depth of coverage when reaching the plateau of the curve on the previous step
Database for taxonomic affiliation
Number of threads