Publication dateMar 9, 2022
Confidentiality public Public
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.
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Input
feature_freq_folder
Feature freq. folder
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Output
Resource set
A set of resources
Resource set
A set of resources
settings
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-v18.202208Number of threads
Type : intDefault value : 2Technical bricks to reuse or customize
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