| name | specificity-screening |
| description | Use when an agent must screen primer candidates or tNGS panel primers for host, near-neighbor, background, or co-infection off-target binding before reporting or ordering primers. |
Specificity Screening
Use this skill after candidate primer generation and before wet-lab export. Production specificity should use BLAST/Bowtie2 databases when available; the bundled helper provides a deterministic local FASTA screen for smoke tests and small curated backgrounds.
Local Screen
python agentskill/scripts/specificity_screen.py kmer-screen \
--primers primer_pairs.csv \
--background-fasta background.fasta \
--max-mismatches 1 \
--seed-length 10 \
--output specificity_report.json
Use --fail-on-hit when any background hit should block release.
Production Checklist
- Screen host genome or transcriptome.
- Screen near-neighbor viruses and same-syndrome pathogens.
- Screen common co-infections and lab controls.
- Use strict 3-prime seed logic for diagnostic primers.
- Report database name, version/date, command, thresholds, and hits.
Do not call a primer production-ready if only target coverage has been checked.
