primer-design
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
The two scanners disagree: Cisco found nothing and SkillSpector says do not install. One of them has a blind spot here; read the skill before trusting either. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates. Use for designing primer pairs, checking existing primers, exon-junction or isoform-specific assays, variant masking, cloning tails, multiplex compatibility, and interpreting Primer-BLAST results. Includes bounded local in-silico PCR and BLAST screening; distinguishes computational candidates from experimentally validated assays.
- Package
- 15 files, 123 KB
- SKILL.md
- 1922 words, 12+ sections
- Code
- Python (5)
- License
- MIT
- Compatibility
- Requires Python 3.11+ and primer3-py 2.3.1 for design and thermodynamics. Local exhaustive screening uses the standard library; BLAST screening additionally needs blastn and makeblastdb on PATH. Network access is needed only for installation, reference retrieval, or external Primer-BLAST.
SKILL.md covers: Primer design and specificity · Choose the workflow · Establish the assay contract · Install and verify · 1. Design candidates · 2. Assess thermodynamics · 3. Screen amplification products · Exhaustive bounded local search · BLAST-assisted local search · Interpret the result · 4. Validate the assay and deliver evidence · Validation and limits of this implementation
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 16 KB |
assets/assay-report-template.md | doc | 2.4 KB |
assets/demo-template.fasta | other | 577 B |
assets/qpcr-config.json | config | 233 B |
assets/requirements.txt | doc | 18 B |
references/design-workflows.md | doc | 10 KB |
references/input-contract.md | doc | 12 KB |
references/sources.md | doc | 4.4 KB |
references/specificity.md | doc | 10 KB |
references/thermodynamics.md | doc | 7.0 KB |
scripts/_common.py | script | 5.5 KB |
scripts/_specificity.py | script | 20 KB |
scripts/check_thermodynamics.py | script | 8.5 KB |
scripts/design_primers.py | script | 15 KB |
scripts/screen_specificity.py | script | 11 KB |
External hosts referenced
pubmed.ncbi.nlm.nih.gov libnano.github.io www.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov www.neb.com academic.oup.com primer3.org arxiv.org media.neb.com pypi.org
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Environment variables referenced
SKILL_DIR SEQUENCE_EXCLUDED_REGION SEQUENCE_INCLUDED_REGION SEQUENCE_PRIMER_PAIR_OK_REGION_LIST
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-primer-design-scan.json
- Badge for your README:
- Request a re-scan