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Introduction Version

Q2 Taxonomy Diversity

TASK
Typing name :  TASK.gws_ubiome.Qiime2TaxonomyDiversity Brick :  gws_ubiome

Computing various diversity index and taxonomy assessement of ASVs

Qiime2TaxonomyDiversity 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 RDP (in version 18).

Minimum required configuration: Digital lab SC2

About RDP: Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data.

Input

feature_freq_folder
Feature freq. folder
Folder

Output

Resource set
A set of resources
Resource set
Resource set
A set of resources
Resource set
Folder
Folder

Configuration

rarefaction_plateau_value

Depth of coverage when reaching the plateau of the curve on the previous step

Type : int

taxonomic_affiliation_database

Optional

Database for taxonomic affiliation

Type : stringAllowed values : RDP-v18.202208  Silva-v13.8  NCBI-16S_rRNA.20220712  GreenGenes-v13.8  Default value : RDP-v18.202208

threads

Optional

Number of threads

Type : intDefault value : 2