qiime2-amplicon SKILL.md skillA
qiime2-amplicon from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/qiime2-amplicon@v1.1Pins v1.1 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/qiime2-amplicon/SKILL.md- Versions recorded
- 2
- Latest version
- v1.1, committed Oct 1, 2026
- First version recorded
- Sep 30, 2026
- Size
- 8,648 bytes
- Repository stars
- 56,497
- License
- MIT
Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap, sample IDs, runtime versions and read retention, and guides selection of compatible taxonomic classifiers.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# QIIME 2 paired-end 16S amplicons Use for a demultiplexed, paired-end 16S assay with known primers, quality encoding, expected insert length, and sample metadata. This bounded workflow imports reads, removes 5′ primers, denoises with DADA2, classifies ASVs using an explicitly supplied classifier, and retains `.qza`/`.qzv` provenance. Do not treat read counts as absolute cell counts or taxonomy assignments as strain identification. ## Establish the assay before running - Confirm Phred+33, read orientation, primer sequences **as sequenced** in forward/reverse reads, and whether primers have already been removed. The bundled runner requires primers still present at the 5′ ends; it anchors Cutadapt matching and discards untrimmed pairs. Already trimmed reads need a direct import → DADA2 workflow with that omission recorded in provenance. - Choose truncation positions from actual per-base quality and error profiles. `trunc-f/r` are positions **after primer removal**. The expected maximum insert length also excludes primers. Require `trunc_f + trunc_r - maximum_insert_length >= 12`; use a margin for length variation. …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/qiime2-amplicon@sha256:605ae0581620f654The line at the top of this page pins the label v1.1, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_t7v27k3zpd2gdobd)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Sep 30, 2026 and Oct 1, 2026, more than one a day.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.1 latest | 2026-10-01 | a92663a | 8,648 B | A | view · diff |
| v1.0 | 2026-09-30 | 9c044a1 | 7,015 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (8648 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_t7v27k3zpd2gdobd GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/qiime2-amplicon GET https://markdownregistry.com/api/v1/blob/605ae0581620f654ca9e12122a2bdb1d62a813841c5fea61b0eacb2031377cf7
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.