Q2NCBIDiversity
Computing various diversity index and taxonomy assessement of ASVs using NCBI 16S
Qiime2TaxonomyDiversityNCBIExtractor 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 NCBI 16S (from 2022.07.12) with reference full-length sequences clustered at 99% sequence similarity.
Minimum required configuration: Digital lab SC2
About NCBI: NCBI 16S RNA database is a collection of 16S ribosomal RNA gene sequences from various organisms stored in the National Center for Biotechnology Information (NCBI) database.
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
stringNCBI-16S_rRNA.20220712 NCBI-16S_rRNA.20220712threads
Number of threads
int2