Add automated rarefaction and/or user-input parameters

bokulich-lab / nf-ducken

Workflow to process amplicon meta-analysis data, from NCBI accession IDs to taxonomic diversity metrics.

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Open lina-kim opened 9 months ago

lina-kim commented 9 months ago

Until this is integrated, downstream analysis of core metrics calculations must be conducted separately after a manual rarefaction step.

Consider various techniques for automation:

Good's coverage as a metric to determine diversity coverage; try point of inflection or threshold?
Observed features
Shannon's diversity is an option, but this is insensitive to rarefaction

lina-kim commented 1 month ago

Consider automatic incorporation using Kneed?