specificity-screening

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.