Q2 Taxonomy Diversity - gws_ubiome

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

A set of resources

Resource set

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 : string

Default value : RDP-v18.202208

threads

Optional

Number of threads

Type : int

Default value : 2