Agent skill

Genomics Qc

Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection.

Apache-2.0Auto-check passedResearch & Science

Install Genomics Qc

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw genomics-qc --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/genomics/genomics-qc .claude/skills/genomics-qc && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "genomics-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc into .claude/skills/genomics-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-qc", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw genomics-qc --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/genomics/genomics-qc .agents/skills/genomics-qc && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "genomics-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc into .agents/skills/genomics-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-qc", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw genomics-qc --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/genomics/genomics-qc .cursor/skills/genomics-qc && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "genomics-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc into .cursor/skills/genomics-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-qc", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/TianGzlab/OmicsClaw.git --path skills/genomics/genomics-qc

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw genomics-qc --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/genomics/genomics-qc .gemini/skills/genomics-qc && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "genomics-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc into .gemini/skills/genomics-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-qc", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw genomics-qc

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/genomics/genomics-qc .github/skills/genomics-qc && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "genomics-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc into .github/skills/genomics-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-qc", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install TianGzlab/OmicsClaw genomics-qc --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/genomics/genomics-qc .opencode/skills/genomics-qc && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "genomics-qc" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-qc into .opencode/skills/genomics-qc/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "genomics-qc", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: genomics-qc
GitHub stars: 161
Token cost: ~1.1k tokens
SKILL.md length: 391 words
Files: 9 (incl. references)
Skills in repo: 88
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection.

Tasks that involve Bioinformatics
SKILL.md covers When to use, Use from a step, API and Methods and parameters, plus 5 more sections
Runs Python scripts from its folder; calls python

What it does

Genomics Qc is an agent skill from TianGzlab/OmicsClaw. Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Skip when working with already-aligned BAMs (use genomics-alignment); peak / variant files are the input (use the relevant downstream skill).

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including reference files (for example `_api.py`, `examples/example_step.py` and `genomics_qc.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Bioinformatics

Example prompts

“/genomics-qc”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 90a3bec. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Genomics Qc loads about 1.1k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 80 tokens; SKILL.md has 391 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~80
When it runs · the whole SKILL.md, loaded when a task matches: ~1.1k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 391 words, ~1,080 tokens.

Download SKILL.mdSave it as .claude/skills/genomics-qc/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.

name: genomics-qc
description: Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Skip when working with already-aligned BAMs (use genomics-alignment); peak / variant files are the input (use the relevant downstream skill).
trigger: sequencing QC, FastQC, read quality, adapter trimming, fastp
tags: genomics, qc, fastq, phred, adapter, fastqc

genomics-qc

When to use

Load this skill for the file-based analysis named in the description. The function library and CLI share the same calculations; no external aligner, assembler, caller or annotation service is started.

Use from a step

python

from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill("genomics-qc")
data = read_input("input.fastq", reader=library.read_records)
result = library.analyze(data)
write_output(result, "tables/result.csv")
write_output(library.distribution_figure(result), "figures/distribution.png")

Run examples/example_step.py through the step runner for a small, hand-worked synthetic fixture. It asserts known summary values. The reader materializes the input in memory; use bounded FASTQ reads or pre-filter large genomic files before loading them.

API

<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->

`read_records(path: str | Path, *, max_reads: int=500000) -> pd.DataFrame`

Read records through read_input(path, reader=library.read_records).

:param path: Input file in the format documented under Inputs and outputs. :param max_reads: CLI default 500000 limits records materialized in memory. :returns: Parsed records as a DataFrame. :raises ValueError: Input values or file structure cannot be parsed.

`analyze(data: pd.DataFrame, *, max_reads: int=500000) -> pd.DataFrame`

Compute qc summaries and return a new table, leaving data unchanged.

:param data: Records containing sequence, quality. :param max_reads: CLI default 500000 limits the analyzed reads. :returns: Result table with diagnostics and summary in attrs['run_info']. :raises ValueError: Required columns are absent or records are empty or invalid.

`run_info(data: pd.DataFrame, *, keep: bool=True) -> dict`

Return analysis diagnostics and summary.

:param data: Result returned by analyze. :param keep: Keep diagnostics by default; the CLI passes False. :returns: Independent diagnostics dictionary. :raises ValueError: analyze has not populated diagnostics.

`distribution_figure(data: pd.DataFrame)`

Plot mean_quality values without writing files.

:param data: Result table containing mean_quality. :returns: Matplotlib Figure. :raises ValueError: The value column is absent or table is empty.

<!-- api:end -->

Show full SKILL.md (150 more words)Show less

Methods and parameters

analyze returns a new DataFrame and leaves the input unchanged. run_info(result) returns the summary and method diagnostics. The CLI passes keep=False so diagnostics do not enter output tables. All calculations are deterministic; synthetic CLI demos retain seed 42.

Gotchas

read_records assumes Phred+33, accepts plain/gzip FASTQ, and rejects incomplete records or mismatched sequence/quality lengths.
analyze measures the first max_reads records (default 500000), tracks at most 300 quality positions and the 20 most frequent read lengths.
run_info()["summary"]["adapter_contamination_pct"] scans the last 20 bases for the first eight bases of two built-in adapter motifs. No trimming occurs.

Inputs and outputs

Input files:

File types: .fastq, .fq

CLI output files:

tables/per_base_quality.csv
tables/qc_metrics.csv
tables/read_length_distribution.csv
report.md
result.json

The library writes no files. Steps use write_output; the CLI owns the listed artifacts. Public figure functions return matplotlib Figures and do not add new CLI outputs.

CLI

bash

python skills/genomics/genomics-qc/genomics_qc.py --input input_file --output results/
python skills/genomics/genomics-qc/genomics_qc.py --demo --output /tmp/genomics_qc_demo

Dependencies

numpy, pandas, matplotlib

Files

SKILL.md and 8 other files (references) in skills/genomics/genomics-qc of TianGzlab/OmicsClaw.

SKILL.md
_api.py
data/example.fastq
examples/example_step.py
genomics_qc.py
references/methodology.md
references/output_contract.md
references/parameters.md
tests/test_api.py

Open the folder on GitHubat commit 90a3bec

Compare with similar skills

Genomics Qc next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Genomics Qc compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Genomics Qc this skillTianGzlab/OmicsClaw	161	—	~1.1k	Automated safety check: Pass	Apache-2.0	2 days ago
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	24 days ago
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	4 days ago
Clinvar Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.9k	Automated safety check: Notes	Apache-2.0	24 days ago
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.4k	Automated safety check: Notes	Apache-2.0	24 days ago

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Questions about Genomics Qc

What does Genomics Qc do?

Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Genomics Qc is an agent skill from TianGzlab/OmicsClaw. Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection.

When should I use Genomics Qc?

Genomics Qc fits situations like: tasks that involve Bioinformatics.

How do I install Genomics Qc in Claude Code?

Run `npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a claude-code`. Or copy the skill folder (skills/genomics/genomics-qc in TianGzlab/OmicsClaw) into .claude/skills/genomics-qc in your project. Claude Code loads it when a task matches its description.

How do I install Genomics Qc in Codex?

Run `npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a codex`. Or copy the skill folder (skills/genomics/genomics-qc in TianGzlab/OmicsClaw) into .agents/skills/genomics-qc in your project. Codex loads it when a task matches its description.

Can I use Genomics Qc in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add TianGzlab/OmicsClaw --skill genomics-qc -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/genomics-qc, .gemini/skills/genomics-qc, .github/skills/genomics-qc and .opencode/skills/genomics-qc in your project.

What does Genomics Qc need to run?

Going by SKILL.md and its folder, Genomics Qc needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Genomics Qc access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Genomics Qc safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Genomics Qc use?

Genomics Qc is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Genomics Qc use?

About 1.1k tokens (SKILL.md is roughly 4.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 496 tokens, read only when the agent opens those files.

What are the alternatives to Genomics Qc?

Skills that share tags, products or a category with Genomics Qc: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Genomics Qc?

TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 2026.

Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Genomics Qc

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

genomics-qc

When to use

Use from a step

API

read_records(path: str | Path, *, max_reads: int=500000) -> pd.DataFrame

analyze(data: pd.DataFrame, *, max_reads: int=500000) -> pd.DataFrame

run_info(data: pd.DataFrame, *, keep: bool=True) -> dict

distribution_figure(data: pd.DataFrame)

Methods and parameters

Gotchas

Inputs and outputs

CLI

See also

Dependencies

Files

Compare with similar skills

Similar skills

More from TianGzlab/OmicsClaw

Related

Questions about Genomics Qc

`read_records(path: str | Path, *, max_reads: int=500000) -> pd.DataFrame`

`analyze(data: pd.DataFrame, *, max_reads: int=500000) -> pd.DataFrame`

`run_info(data: pd.DataFrame, *, keep: bool=True) -> dict`

`distribution_figure(data: pd.DataFrame)`