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QIIME 2 16S Amplicon Workflow

Runs paired-end 16S amplicon processing in QIIME 2 with checks and provenance records

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
3 files

What it does

This skill guides an AI agent through processing paired-end 16S rRNA sequencing reads (a common way to identify which microbes are in a sample) using QIIME 2, a standard bioinformatics toolkit. It checks the input files, primer sequences, read lengths and sample IDs before running, then denoises reads into ASVs (exact sequence variants) and assigns taxonomy using a classifier the user supplies. It keeps provenance records so results can be traced back to their inputs.

Great for

  • Microbiome researchers who have demultiplexed paired-end 16S reads with known primers
  • Bioinformatics students learning the QIIME 2 amplicon workflow and its quality checks
  • Lab staff who need reproducible, checksummed run records for amplicon data

Skip it if

  • Reads that are not 16S amplicons or have unknown primers, since the checks and classifier choices assume a known assay and results would be unreliable
  • Interpreting taxonomy as confirmed strain identity or read counts as absolute cell counts, which the skill itself warns against
  • Sensitive human data run through an unvetted classifier file, since the skill warns that serialized sklearn classifiers should only be loaded from trusted sources

Try asking

  • “Validate my paired-end 16S manifest and primer settings before I run QIIME 2”
  • “Run the amplicon workflow on my samples with this classifier file and 4 threads”
  • “Check whether my truncation lengths leave enough overlap for my 300 bp amplicons”
  • “Explain the retention-qc.json output from my last QIIME 2 run”
Step-by-step guide: how to use QIIME 2 16S Amplicon WorkflowInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 3 original files, the MIT licence and an attribution note.

    qiime2-amplicon.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip qiime2-amplicon.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip qiime2-amplicon.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Run the validate command first; it checks the manifest, metadata and overlap without needing QIIME installed.
  • Choose truncation lengths from your own quality profiles or a pilot run, since the example primers and lengths are illustrative only.
  • Keep the original .qza/.qzv artifacts rather than exporting to CSV or BIOM, because exports lose provenance.

What's inside

  • references/runtime-and-interpretation.md
  • scripts/amplicon_workflow.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.