bakta-genome-annotation SKILL.md skillA
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
bakta-genome-annotation 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/bakta-genome-annotation@git:20261004.abbbdf3Pins git:20261004.abbbdf3 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/bakta-genome-annotation/SKILL.md- Versions recorded
- 2
- Latest version
- git:20261004.abbbdf3, committed Oct 4, 2026
- First version recorded
- May 17, 2026
- Size
- 23,530 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.
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
# Bakta Genome Annotation ## Overview Bakta is a command-line pipeline for rapid, standardized annotation of bacterial and archaeal genomes and plasmids. It combines Prodigal for CDS prediction, tRNAscan-SE/Aragorn/Barrnap/Infernal for non-coding RNA, PILER-CR/PILERCR for CRISPR detection, and a tiered DIAMOND/HMM search against a curated UniRef100 + IPS/UPS database to assign gene names, EC numbers, GO terms, and COG categories. Bakta produces NCBI-compatible outputs (GFF3, GenBank, EMBL, INSDC-formatted FASTA, plus a JSON summary and a circular Circos plot) for a typical 5 Mb genome in 5–15 minutes on 8 CPUs. ## When to Use - Annotating bacterial or archaeal genome assemblies (Illumina, PacBio, Nanopore) with NCBI-compatible locus tags and product names - Annotating plasmids and other circular replicons separately with `--plasmid` and `--complete` flags - Producing JSON-structured annotation outputs that can be parsed without GenBank or GFF3 detours - Generating a publication-ready circular genome plot via the bundled `bakta_plot` command - Annotating MAGs (metagenome-assembled genomes) with `--meta` to disable Prodigal training …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bakta-genome-annotation@sha256:96cec1bdfddb5a8dThe line at the top of this page pins the label git:20261004.abbbdf3, 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_6ar4velcs2fs7uvk)
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Versions
The registry has recorded 2 versions of this file, between May 17, 2026 and Oct 4, 2026, about one every 140 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261004.abbbdf3 latest | 2026-10-04 | abbbdf3 | 23,530 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 21,537 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 (23530 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_6ar4velcs2fs7uvk GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bakta-genome-annotation GET https://markdownregistry.com/api/v1/blob/96cec1bdfddb5a8d1b1f429fc24b8c864d677cf9e097c5774fb7488de5e020ef
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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.
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