Version Compatibility

Reference examples tested with: DADA2 1.30+, cutadapt 4.4+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Amplicon Processing with DADA2

"Process my 16S amplicon data to get ASVs" → Denoise amplicon sequencing reads into exact amplicon sequence variants (ASVs) through quality filtering, error model learning, and chimera removal.

• R: dada2::filterAndTrim() → learnErrors() → dada() → removeBimeraDenovo()

Complete DADA2 Workflow

library(dada2)