bio-metagenomics-abundance SKILL.md skillA
bio-metagenomics-abundance 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-metagenomics-abundance@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/abundance-estimation/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260614.5d4591c, committed Jun 14, 2026
- First version recorded
- May 17, 2026
- Size
- 16,564 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Turns shotgun classifier output into a defensible abundance table with Bracken Bayesian re-estimation, then compositional treatment (CLR, zero handling), library-size normalization, reference-frame differential abundance, and optional absolute quantification. Covers why a relative-abundance change is not a change, why Bracken read fractions and MetaPhlAn percentages are different physical quantities, the silent -r read-length bias, the genome-size confound no library-size method fixes, and the…
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: Bracken 2.9+, Kraken2 2.1.3+, pandas 2.2+, scikit-bio 0.6+, R zCompositions 1.5+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `bracken -h`, `bracken-build -h` to confirm flags and defaults
- Python: `pip show <package>` then `help(module.function)` to check signatures
- R: `packageVersion('zCompositions')` then `?cmultRepl` 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.
The Bracken `databaseRLENmers.kmer_distrib` is built per database at a fixed read length and MUST match both the Kraken2 database and the actual (post-trim) read length; `-r` is not auto-detected and a mismatch silently biases every species fraction. Bracken needs the default Kraken2 report format, not mpa-style.
# Abundance Estimation
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-metagenomics-abundance@sha256:cea7351a6da9164fThe 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_h7bpgliadplndhyo)
3 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 | 16,564 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 5,890 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 5,892 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 (16564 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_h7bpgliadplndhyo GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-metagenomics-abundance GET https://markdownregistry.com/api/v1/blob/cea7351a6da9164f0c9ed04e198525482b29c0b5592f85abc11aa4dde120de14
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.