bio-alignment-indexing SKILL.md skillA
bio-alignment-indexing 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-alignment-indexing@git:20260712.2ff971bPins git:20260712.2ff971b 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/alignment-indexing/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260712.2ff971b, committed Jul 12, 2026
- First version recorded
- May 17, 2026
- Size
- 9,726 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
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: pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# Alignment Indexing
Create indices for random access to alignment files using samtools and pysam.
**"Index a BAM file"** -> Create a .bai/.csi index enabling random access to genomic regions.
- CLI: `samtools index file.bam`
- Python: `pysam.index('file.bam')`
## Index Types
| Index | Extension | Max contig | Bin shift | When required |
|-------|-----------|-----------|-----------|---------------|
| BAI | `.bai` / `.bam.bai` | 2^29 bp ≈ 537 Mbp | fixed (16 kb) | Default for human, mouse, fly, fish |
| CSI | `.csi` / `.bam.csi` | 2^(min_shift + depth*3) | configurable via `-m` | **Required** for any contig >537 Mbp |
| CRAI | `.crai` / `.cram.crai` | chunk-based | n/a | CRAM only |
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-alignment-indexing@sha256:bbca68b346a6a043The line at the top of this page pins the label git:20260712.2ff971b, 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_r6herw53lrndoqpk)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 17, 2026 and Jul 12, 2026, about one every 19 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260712.2ff971b latest | 2026-07-12 | 2ff971b | 9,726 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 9,578 B | A | view · diff |
| git:20260528.89ddef6 | 2026-05-28 | 89ddef6 | 9,579 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 9,500 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 (9726 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_r6herw53lrndoqpk GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-alignment-indexing GET https://markdownregistry.com/api/v1/blob/bbca68b346a6a043dd60ba8e526f68740fb5103fe5ff930c63c42b13034a42d4
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.
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