New: 98,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Genomics Alignment

by TianGzlab in TianGzlab/OmicsClaw

Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2…

Apache-2.0Auto-check passedResearch & Science

Install Genomics Alignment

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

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

GitHub CLI
$ gh skill install TianGzlab/OmicsClaw genomics-alignment --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-alignment .claude/skills/genomics-alignment && 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/

Facts

Skill name
genomics-alignment
GitHub stars
161
Token cost
~999 tokens
SKILL.md length
346 words
Files
9 (incl. references)
Skills in repo
88
Repo updated
First seen
Licence
Apache-2.0

At a glance

Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2…

  • 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 Alignment is an agent skill from TianGzlab/OmicsClaw. Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2); convert a BAM with samtools view -h first. Skip when running the alignment step itself; only FASTQ-level QC is needed (use genomics-qc).

Its SKILL.md is about 1000 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_alignment.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-alignment”

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 Alignment loads about 999 tokens when it runs, and up to ~1.5k if it reads all its reference files. Until then it costs about 92 tokens; SKILL.md has 346 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~92
When it runs · the whole SKILL.md, loaded when a task matches
~999
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.5k

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). 346 words, ~999 tokens.

Download SKILL.mdSave it as .claude/skills/genomics-alignment/SKILL.md (or your agent's skills folder). This skill also uses 8 other files; get the full folder from GitHub.
name
genomics-alignment
description
Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2); convert a BAM with samtools view -h first. Skip when running the alignment step itself; only FASTQ-level QC is needed (use genomics-qc).
trigger
alignment, BWA, Bowtie2, Minimap2, map reads
tags
genomics, alignment, bam, sam, bwa, bowtie2, minimap2

genomics-alignment

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-alignment")
data = read_input("input.sam", 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) -> pd.DataFrame

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

:param path: Input file in the format documented under Inputs and outputs.

:returns: Parsed records as a DataFrame. :raises ValueError: Input values or file structure cannot be parsed.

analyze(data: pd.DataFrame) -> pd.DataFrame

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

:param data: Records containing flag, mapq, tlen.

: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.

Show full SKILL.md (156 more words)Show less
distribution_figure(data: pd.DataFrame)

Plot mapping_rate_pct values without writing files.

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

<!-- api:end -->

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 accepts text SAM, not binary BAM/CRAM; convert those upstream. No aligner or samtools is invoked.
  • run_info()["summary"] excludes secondary and supplementary alignments from primary-read metrics; insert sizes count both mates, matching the legacy CLI.

Inputs and outputs

Input files:

  • File types: .sam

CLI output files:

  • tables/alignment_stats.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-alignment/genomics_alignment.py --input input_file --output results/
python skills/genomics/genomics-alignment/genomics_alignment.py --demo --output /tmp/genomics_alignment_demo

See also

  • references/parameters.md
  • references/methodology.md
  • references/output_contract.md

Dependencies

numpy, pandas, matplotlib

© TianGzlab, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

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

  • SKILL.md
  • _api.py
  • data/example.sam
  • examples/example_step.py
  • genomics_alignment.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 Alignment 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 Alignment compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Genomics Alignment this skillTianGzlab/OmicsClaw161—~999Automated safety check: PassApache-2.0
Dbsnp Databasegoogle-deepmind/science-skills3.2k3 repos~3.4kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

Similar skills

  • Dbsnp Database

    google-deepmind/science-skills

    A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.

    3.2k GitHub starsUsed in 3 repos~3.4k tokens
    Research & ScienceAuto-check: notes

  • Metabolic Study Planner

    aiming-lab/AutoResearchClaw

    Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.

    15k GitHub stars~1.9k tokensUpdated 1 mo ago
    Research & ScienceAuto-check passed

  • 13C Metabolic Flux Analysis

    K-Dense-AI/scientific-agent-skills

    Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.

    48k GitHub starsUsed in 1 repo~3.2k tokens
    Research & ScienceAuto-check passed

  • Alphagenome Single Variant Analysis

    google-deepmind/science-skills

    Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.

    3.2k GitHub starsUsed in 2 repos~3k tokens
    Research & ScienceAuto-check: notes

  • MFA Pipeline Orchestrator

    aiming-lab/AutoResearchClaw

    Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.

    15k GitHub stars~923 tokensUpdated 1 mo ago
    Research & ScienceAuto-check passed

  • Singlecell Qc

    xuzhougeng/wisp-science

    A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.

    1k GitHub stars~1.6k tokensUpdated today
    Research & ScienceAuto-check passed

More from TianGzlab/OmicsClaw

All 88 skills in this repo

  • Bulkrna De

    TianGzlab/OmicsClaw

    Load when comparing gene expression between two conditions in bulk RNA-seq count data.

    161 GitHub starsUsed in 1 repo~867 tokens
    Auto-check passed

  • Bulkrna Cosinor Rhythm

    TianGzlab/OmicsClaw

    Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.

    161 GitHub stars~840 tokensUpdated today
    Auto-check passed

  • Bulkrna Qc

    TianGzlab/OmicsClaw

    Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE.

    161 GitHub starsUsed in 1 repo~789 tokens
    Auto-check passed

  • Sc Fastq Qc

    TianGzlab/OmicsClaw

    Load when checking raw single-cell FASTQ read quality (Phred / GC / adapter / length) before counting.

    161 GitHub starsUsed in 1 repo~1k tokens
    Auto-check passed

  • Sc Filter

    TianGzlab/OmicsClaw

    Load when removing low-quality cells and lowly-detected genes from a single-cell AnnData using QC-derived thresholds or tissue presets.

    161 GitHub starsUsed in 1 repo~2.1k tokens
    Auto-check passed

  • Sc Markers

    TianGzlab/OmicsClaw

    Load when ranking cluster-level marker genes from a clustered single-cell AnnData via Scanpy Wilcoxon / t-test / logreg or COSG specificity.

    161 GitHub starsUsed in 1 repo~2.2k tokens
    Auto-check passed

Categories

Questions about Genomics Alignment

What does Genomics Alignment do?

Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2…. Genomics Alignment is an agent skill from TianGzlab/OmicsClaw. Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2); convert a BAM with samtools view -h first.

When should I use Genomics Alignment?

Genomics Alignment fits situations like: tasks that involve Bioinformatics.

How do I install Genomics Alignment in Claude Code?

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

How do I install Genomics Alignment in Codex?

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

Can I use Genomics Alignment 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-alignment -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-alignment, .gemini/skills/genomics-alignment, .github/skills/genomics-alignment and .opencode/skills/genomics-alignment in your project.

What does Genomics Alignment need to run?

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

Does Genomics Alignment 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 Alignment 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 Alignment use?

Genomics Alignment 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 Alignment use?

About 999 tokens (SKILL.md is roughly 4k 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 458 tokens, read only when the agent opens those files.

What are the alternatives to Genomics Alignment?

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

Who maintains Genomics Alignment?

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.