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:20260520.7a7a671Pins git:20260520.7a7a671 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/bio-alignment-indexing/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260520.7a7a671, committed May 20, 2026
- First version recorded
- May 17, 2026
- Size
- 6,076 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
<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA --> # Alignment Indexing Create indices for random access to alignment files using samtools and pysam. ## Index Types | Index | Extension | Use Case | |-------|-----------|----------| | BAI | `.bai` | Standard BAM index, chromosomes < 512 Mbp | | CSI | `.csi` | Large chromosomes, custom bin sizes | | CRAI | `.crai` | CRAM index | ## samtools index ### Create BAI Index ```bash samtools index input.bam # Creates input.bam.bai ``` ### Create CSI Index ```bash samtools index -c input.bam # Creates input.bam.csi ``` ### Specify Output Name ```bash samtools index input.bam output.bai ``` ### Multi-threaded Indexing ```bash samtools index -@ 4 input.bam ``` ### Index CRAM ```bash samtools index input.cram # Creates input.cram.crai ``` ## Index Requirements Indexing requires coordinate-sorted files: ```bash # Check sort order …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-alignment-indexing@sha256:6310d2051cb39c69The line at the top of this page pins the label git:20260520.7a7a671, 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_zmzl7bbom4dviig2)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between May 17, 2026 and May 20, 2026, about one every 4 days. Its first recorded version is graded C and its latest A.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260520.7a7a671 latest | 2026-05-20 | 7a7a671 | 6,076 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 6,075 B | C | 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 (6076 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 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zmzl7bbom4dviig2 GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-alignment-indexing GET https://markdownregistry.com/api/v1/blob/6310d2051cb39c697418bc4a35d77ce92fd9551a0c017c45c2462e21be617ec0
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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