specificity-screening

Name: specificity-screening
Author: KevinSpringer1

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How to install specificity-screening?

kevinspringer1/conserved-primer-design/specificity-screening

$npx -y skills add KevinSpringer1/conserved-primer-design --skill specificity-screening

Installs into the current project.

Summary

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.

Files · 1

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SKILL.md

1	# Specificity Screening
2
3	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.
4
5	## Local Screen
6
7	```bash
8	python agentskill/scripts/specificity_screen.py kmer-screen \
9	--primers primer_pairs.csv \
10	--background-fasta background.fasta \
11	--max-mismatches 1 \
12	--seed-length 10 \
13	--output specificity_report.json
14	```
15
16	Use `--fail-on-hit` when any background hit should block release.
17
18	## Production Checklist
19
20	- Screen host genome or transcriptome.
21	- Screen near-neighbor viruses and same-syndrome pathogens.
22	- Screen common co-infections and lab controls.
23	- Use strict 3-prime seed logic for diagnostic primers.
24	- Report database name, version/date, command, thresholds, and hits.
25
26	Do not call a primer production-ready if only target coverage has been checked.

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specificity-screening

30stars0forks

View on GitHub

How to install specificity-screening?

kevinspringer1/conserved-primer-design/specificity-screening

$npx -y skills add KevinSpringer1/conserved-primer-design --skill specificity-screening

Installs into the current project.

Summary

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.

Files · 1

View on GitHub

SKILL.md

1	# Specificity Screening
2
3	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.
4
5	## Local Screen
6
7	```bash
8	python agentskill/scripts/specificity_screen.py kmer-screen \
9	--primers primer_pairs.csv \
10	--background-fasta background.fasta \
11	--max-mismatches 1 \
12	--seed-length 10 \
13	--output specificity_report.json
14	```
15
16	Use `--fail-on-hit` when any background hit should block release.
17
18	## Production Checklist
19
20	- Screen host genome or transcriptome.
21	- Screen near-neighbor viruses and same-syndrome pathogens.
22	- Screen common co-infections and lab controls.
23	- Use strict 3-prime seed logic for diagnostic primers.
24	- Report database name, version/date, command, thresholds, and hits.
25
26	Do not call a primer production-ready if only target coverage has been checked.

People who liked this also viewed

6 picks

Type