bio-alignment-indexing

bio-alignment-indexing is a skill for Claude Code, Codex from FridrichMethod/awesome-skills. It costs 41 tokens per session (2,804 once invoked), scanned A, original, no licence file.

A method for creating and using lookup indexes for BAM and CRAM files, which store DNA sequencing alignments. It uses samtools and pysam to find reads in specific genomic regions without scanning the whole file.

In plain words
What is it for?
It helps prepare alignment files for random access and fetch reads from selected parts of a genome.
Why use it?
Without an index, retrieving one region from a large alignment file can require reading much more data than needed.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit It helps prepare alignment files for random access and fetch reads from selected parts of a genome.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/fridrichmethod/awesome-skills/alignment-indexing
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add FridrichMethod/awesome-skills --skill alignment-indexing
Clone the repo
git clone --depth 1 https://github.com/FridrichMethod/awesome-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for bio-alignment-indexing

README.md
[![agentmods](https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-indexing/github.svg)](https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-indexing)
Your own site
<a href="https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-indexing"><img src="https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-indexing/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for bio-alignment-indexing

Your own site · 80×15
<a href="https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-indexing"><img src="https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-indexing.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 41 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,804 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00041 $0.02804
Opus 5.5 $0.00016 $0.01122
Sonnet 5.5 $0.00008 $0.00561
Haiku 4.5 $0.00004 $0.00280

Measured 1mo ago against content hash bbca68b346a6, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

bio-alignment-indexing scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/fetch_regions.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

count = sum(1 for _ in bam.fetch(chrom, start, end))
skills/alignment-indexing/SKILL.md · 312 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago First seen · 312 lines · 41 tokens per session scan A bbca68b346a6

Subscribe to this mod's changes

bio-alignment-indexing is a skill published in the GitHub repository FridrichMethod/awesome-skills (15 stars, last pushed today), with no licence file. It adds 41 tokens to every session and 2,804 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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