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Gtars Genomic Interval Toolkit

Guides safe local genomic interval analysis, overlaps, coverage and tokenization with Gtars

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
15 files

What it does

Gives the agent a careful workflow for working with genomic interval files (BED-style regions) using the Gtars library in Python, Rust, or its command-line tool. Before analysis, the agent is told to check coordinates, assembly, chromosome names and strand, and to run bundled local validators that inspect files without changing them. It also covers set operations, overlaps, coverage, tokenization and refget/BEDbase planning, with explicit approval required for network access or downloads.

Great for

  • Bioinformaticians who need to validate and compare BED interval files with reproducible steps
  • Developers building genomics pipelines in Python or Rust who want documented Gtars API usage
  • Analysts preparing coverage or overlap summaries who need resource limits and provenance recorded

Skip it if

  • Clinical or patient-facing decisions, since the skill is a technical tool and its outputs need expert validation
  • Users who want a fully automatic one-click analysis without reviewing installed code, because installing Gtars compiles or loads native code
  • Workflows that rely on remote data fetching without approval, since remote constructors and refget/BEDbase caching need explicit network and storage approval

Try asking

  • “Validate data.bed.gz against GRCh38 chrom sizes and check it is sorted”
  • “Compute overlaps and counts between two interval sets using Gtars in Python”
  • “Plan a coverage/bigWig generation run with resource limits using the preflight script”
  • “Build a tokenization manifest for genomic regions for a machine learning dataset”
Step-by-step guide: how to use Gtars Genomic Interval ToolkitInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 15 original files, the MIT licence and an attribution note.

    gtars.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip gtars.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip gtars.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Install gtars into an isolated virtual environment and verify the version and checksums before running any analysis
  • Pilot the workflow on a small synthetic file first and set explicit limits on bytes, records, memory and time
  • Specify your assembly, chromosome naming and whether overlapping or adjacent intervals should be merged, since the skill says these policies must be chosen explicitly

What's inside

  • references/cli.md
  • references/coverage.md
  • references/overlap.md
  • references/python-api.md
  • references/refget.md
  • references/tokenizers.md
  • scripts/__init__.py
  • scripts/_common.py
  • scripts/artifact_inspector.py
  • scripts/bed_validator.py
  • scripts/coverage_preflight.py
  • scripts/execution_plan.py
  • scripts/refget_digest_plan.py
  • scripts/tokenizer_manifest.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.