prokka-genome-annotation SKILL.md skillA
prokka-genome-annotation from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/prokka-genome-annotation@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/annotation/prokka-genome-annotation/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 24,422 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.
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
# Prokka Genome Annotation ## Overview Prokka is a command-line pipeline for rapid annotation of prokaryotic genomes (bacteria, archaea, and viruses). It uses a tiered search strategy: protein-coding genes (CDS) are predicted with Prodigal and searched first against a genus-specific database, then RefSeq proteins, then Pfam/TIGRFAMs HMMs. Non-coding RNA genes (rRNA, tRNA, tmRNA) are identified with Barrnap, Aragorn, and Infernal. Prokka processes a single FASTA assembly in minutes and outputs a comprehensive annotation in GFF3, GenBank, FASTA, and tabular formats. ## When to Use - Annotating a newly assembled bacterial or archaeal genome from Illumina, PacBio, or Nanopore assemblies - Getting functional protein annotations (CDS with product names, EC numbers, GO terms) from a draft or complete genome - Preparing annotation files for downstream comparative genomics (Roary pan-genome, OrthoFinder) - Annotating viral or phage genomes when kingdom-specific databases are important - Performing metagenome-assembled genome (MAG) annotation with the `--metagenome` flag - Parsing annotated outputs in Python with BioPython for downstream sequence or feature analysis …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/prokka-genome-annotation@sha256:08d400632f1a53c9The line at the top of this page pins the label git:20260929.7a7d60f, 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_2qu3wms5lptexjvg)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 62 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 24,422 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 24,471 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 22,478 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 (24422 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_2qu3wms5lptexjvg GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/prokka-genome-annotation GET https://markdownregistry.com/api/v1/blob/08d400632f1a53c9d5be31c93c8e0be6bf7d06a886b3911e22c8d934a31426d3
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.