bio-alignment-filtering

bio-alignment-filtering is a skill for Claude Code, Codex from FridrichMethod/awesome-skills. It costs 44 tokens per session (4,295 once invoked), scanned A, original, no licence file.

A method for filtering sequence alignments, which are matches between biological reads and a reference sequence. It uses samtools view and pysam to select reads by flags, mapping quality, or genomic regions.

In plain words
What is it for?
Selecting specific reads, excluding low-quality alignments, and limiting alignment files to target regions.
Why use it?
It helps remove unreliable matches and extract only the biological data relevant to a particular analysis.

Skill for Claude CodeCodex

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.

agentmods
npx agentmods add skills/fridrichmethod/awesome-skills/alignment-filtering
Any agent
npx skills add FridrichMethod/awesome-skills --skill alignment-filtering
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-filtering

README.md
[![agentmods](https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-filtering.svg)](https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-filtering)
Your own site
<a href="https://agentmods.dev/skills/fridrichmethod/awesome-skills/alignment-filtering"><img src="https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/alignment-filtering.svg" alt="Measured on agentmods" height="20"></a>
Per session 44 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,295 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. Scan, not verified.
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 $0.00044 $0.04295
Opus 5 $0.00022 $0.02148
Sonnet 5 $0.00009 $0.00859
Haiku 4.5 $0.00004 $0.00430

Measured 4d ago against content hash e24ea6628923, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

bio-alignment-filtering 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 4d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/filter_bam.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.

for read in infile.fetch(chrom, start, end):
skills/alignment-filtering/SKILL.md · 411 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

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. 4d ago First seen · 411 lines · 44 tokens per session scan A e24ea6628923

Subscribe to this mod's changes

bio-alignment-filtering is a skill published in the GitHub repository FridrichMethod/awesome-skills (14 stars, last pushed 5d ago), with no licence file. It adds 44 tokens to every session and 4,295 once invoked, about $0.0002 per session on Opus 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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