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16S / Targeted Amplicon Sequencing

Domain key: amplicon

Amplicon sequencing targets specific marker genes (16S rRNA, ITS) to profile microbial communities. Codaris builds QIIME2-wrapped pipelines with DADA2 denoising for exact ASV inference.

Step Tool Notes
Primer trimming Cutadapt Remove primers before denoising
Denoising DADA2 Exact ASVs — preferred over OTU clustering
Framework QIIME2 Reproducible wrapper for the full workflow
Functional prediction PICRUSt2 Predict functional pathways from 16S

Best Practices Enforced

  • Cutadapt primer removal is mandatory — primers left in reads corrupt DADA2 error models
  • DADA2 is used for ASV inference (not OTU clustering with VSEARCH/QIIME1 methods)
  • SILVA or Greengenes2 taxonomy databases are used for 16S classification — Codaris prompts for the database path
  • QIIME2 wraps the workflow for reproducibility and .qza artifact traceability

Example Prompts

Build a 16S rRNA amplicon pipeline for mouse gut microbiome.
V3-V4 region, paired-end reads. Use SILVA 138 for taxonomy.

codaris > I have ITS amplicon data for fungal community profiling.
          Use Cutadapt for primer removal and DADA2 for denoising.

Build a 16S pipeline with DADA2 denoising and PICRUSt2
functional prediction. Samples are human oral microbiome.