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Life Sciences NGS Analysis

Guided NGS intake, local execution, and public-pipeline routing for BCL, FASTQ, DNA variant, RNA-seq, single-cell, epigenomics, amplicon, and metagenomics analyses, with deeper decision skills for high-risk assay branches.

Pre-approved tools

No allowed-tools or tools list in its SKILL.md, command or agent files, so the agent asks before using tools as usual.

Hooks

No hooks.

MCP servers and apps

None.

Bundled code

31 code files (Python):

• ngs-analysis/tests/test_bulk_rnaseq_counts_qc_runner.py
• ngs-analysis/tests/test_new_backend_planners.py
• ngs-analysis/tests/test_scrnaseq_post_count_qc_runner.py
• ngs-analysis/tests/test_bcl_to_fastq_runner.py
• ngs-analysis/tests/test_ngs_preflight.py
• ngs-analysis/scripts/run_scrnaseq_fastq_to_count.py
• ngs-analysis/scripts/ngs_visualization_utils.py
• ngs-analysis/scripts/run_dna_variant_calling.py
• ngs-analysis/scripts/ngs_planner_utils.py
• ngs-analysis/scripts/ngs_reference_manager.py
• ngs-analysis/scripts/run_atacseq_peaks_qc.py
• ngs-analysis/scripts/run_dna_germline_variants.py
• ngs-analysis/scripts/ngs_run_utils.py
• ngs-analysis/scripts/run_amplicon_microbiome.py
• ngs-analysis/scripts/ngs_preflight.py
• and 16 more

Network calls

1 file with a network call pattern. First match per file:

• plugins/ngs-analysis/scripts/ngs_visualization_utils.py:18

  import urllib.request

Starts other programs

10 files. First match per file:

• plugins/ngs-analysis/scripts/run_scrnaseq_fastq_to_count.py:80

  result = subprocess.run(

• plugins/ngs-analysis/scripts/ngs_visualization_utils.py:197

  process = subprocess.Popen(  # noqa: S603

• plugins/ngs-analysis/scripts/ngs_run_utils.py:137

  result = subprocess.run(

• plugins/ngs-analysis/scripts/run_amplicon_microbiome.py:354

  result = subprocess.run(

• plugins/ngs-analysis/scripts/ngs_preflight.py:52

  result = subprocess.run(

Credentials referenced

No key, token or secret environment variable found in code or MCP config.

Static scan of commit 0722921 on 2026-10-27. Signals are patterns found in the files, not a verdict: a network call can be the whole point of a skill. Read the linked lines before you decide. How the scan works.