bio-microbiome-amplicon-processing SKILL.md skillA
bio-microbiome-amplicon-processing from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-microbiome-amplicon-processing@git:20260614.5d4591cPins git:20260614.5d4591c in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/amplicon-processing/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260614.5d4591c, committed Jun 14, 2026
- First version recorded
- May 17, 2026
- Size
- 22,630 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removing primers with cutadapt (--discard-untrimmed), learning a per-run error model (filterAndTrim -> learnErrors -> dada -> mergePairs), merging run-level tables with mergeSequenceTables, then one removeBimeraDenovo. Covers why primers come OFF before truncation, why the error model is per-run, truncLen as a merge-overlap detection budget (V4 vs V3-V4), DADA2 vs Deblur and q2-dada2…
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
## Version Compatibility
Reference examples tested with: DADA2 1.30+, cutadapt 4.6+, ITSxpress 2.0+, QIIME2 2024.2+.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
- Python: `pip show <package>` then `help(module.function)` to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
The error model is a PER-RUN artifact, not a version: `learnErrors` is fit to one sequencing run (flowcell/chemistry/instrument). Multi-run studies run the per-run inference separately, then `mergeSequenceTables`, then a single chimera removal - never pool FASTQs across runs before `learnErrors`. DADA2 `dada()` defaults (`OMEGA_A` 1e-40, `mergePairs` `minOverlap` 12) and QIIME2 plugin flag spellings drift between releases; confirm with `?dada` and `qiime dada2 --help`.
# Amplicon Processing with DADA2
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-microbiome-amplicon-processing@sha256:998ef8233364845dThe line at the top of this page pins the label git:20260614.5d4591c, 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_ssihf6uw27rfkplk)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 17, 2026 and Jun 14, 2026, about one every 14 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260614.5d4591c latest | 2026-06-14 | 5d4591c | 22,630 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 4,376 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 4,380 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 (22630 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
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ssihf6uw27rfkplk GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-microbiome-amplicon-processing GET https://markdownregistry.com/api/v1/blob/998ef8233364845de702483cf6651237cd1efc45bb5ee4adc932ae4b08db3d29
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.