Determine appropriate chimera-checking method for DADA2 and VSEARCH

bokulich-lab / nf-ducken

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

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Determine appropriate chimera-checking method for DADA2 and VSEARCH #23

Open lina-kim opened 2 years ago

lina-kim commented 2 years ago

Exposed all relevant chimera-checking parameters for dada2 denoise, and incorporated vsearch uchime-ref. Testing to see which are most helpful for our study.

lina-kim commented 2 years ago

Data waiting to be explored:

dada2 denoise run with --p-chimera-method of none, consensus, and pooled
All three DADA2 outputs run through vsearch uchime-ref

Also will be helpful to explore error logs and incorporate tests for vsearch uchime-ref wrapper.