tngs-panel-design

Name: tngs-panel-design
Author: KevinSpringer1

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How to install tngs-panel-design?

kevinspringer1/conserved-primer-design/tngs-panel-design

$npx -y skills add KevinSpringer1/conserved-primer-design --skill tngs-panel-design

Installs into the current project.

Summary

Use when an agent must turn primer pair candidates into a tiled or multiplex tNGS amplicon panel with target coverage, overlap, selected pairs, and uncovered gap reporting.

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SKILL.md

1	# tNGS Panel Design
2
3	Use this skill when the deliverable is a panel rather than one diagnostic amplicon. Inputs should already be curated, aligned, and primer-QC checked.
4
5	## Greedy Panel Selection
6
7	Candidate CSV/JSON must include `pair_id`, `forward_sequence`, `reverse_sequence`, `amplicon_start`, and `amplicon_end`.
8
9	```bash
10	python agentskill/scripts/primer_panel_qc.py design-panel \
11	--candidates candidate_pairs.csv \
12	--genome-length 30000 \
13	--required-overlap 20 \
14	--min-coverage 0.95 \
15	--output panel_plan.json \
16	--csv-output selected_panel.csv
17	```
18
19	## Review Criteria
20
21	- Check `coverage_fraction` and every gap in `panel_plan.json`.
22	- Confirm amplicon size matches the sequencing platform and sample quality.
23	- Confirm selected pairs still pass wet-lab QC and specificity screening.
24	- Run pool assignment before wet-lab export.

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