reference-dataset-curation

Name: reference-dataset-curation
Author: KevinSpringer1

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How to install reference-dataset-curation?

kevinspringer1/conserved-primer-design/reference-dataset-curation

$npx -y skills add KevinSpringer1/conserved-primer-design --skill reference-dataset-curation

Installs into the current project.

Summary

Use when an agent must select, filter, deduplicate, and document NCBI/GenBank/reference viral genomes before alignment, primer design, PhyloGuide, or tNGS panel design.

Files · 1

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SKILL.md

1	# Reference Dataset Curation
2
3	Use this skill after taxonomy curation and before MAFFT or Agent API submission. The goal is a reproducible accession manifest, not just a broad NCBI query.
4
5	## Workflow
6
7	1. Start from literature/curated accession lists when possible; use broad NCBI queries only as a fallback.
8	2. Record accession, species, genotype/subtype/clade, host, country, date, completeness, length, ambiguous-base fraction, and source.
9	3. Filter by the user’s scope and quality thresholds.
10	4. Deduplicate exact accession and exact sequence hash.
11	5. Keep rejected records and reasons.
12
13	```bash
14	python agentskill/scripts/curate_references.py curate-accessions \
15	--metadata-csv accession_metadata.csv \
16	--taxonomy-json taxonomy.json \
17	--species "Target virus" \
18	--host "target host" \
19	--min-length 1000 \
20	--max-n-fraction 0.05 \
21	--require-complete \
22	--dedupe-by-sequence \
23	--output accession_manifest.json \
24	--accepted-csv accession_accepted.csv \
25	--rejected-csv accession_rejected.csv
26	```
27
28	## Acceptance Gate
29
30	Proceed only when:
31
32	- accepted accessions cover the required groups and time/region scope;
33	- all filters are recorded in `accession_manifest.json`;
34	- rejected records are available for audit;
35	- accession versions are pinned where available.

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reference-dataset-curation

30stars0forks

View on GitHub

How to install reference-dataset-curation?

kevinspringer1/conserved-primer-design/reference-dataset-curation

$npx -y skills add KevinSpringer1/conserved-primer-design --skill reference-dataset-curation

Installs into the current project.

Summary

Use when an agent must select, filter, deduplicate, and document NCBI/GenBank/reference viral genomes before alignment, primer design, PhyloGuide, or tNGS panel design.

Files · 1

View on GitHub

SKILL.md

1	# Reference Dataset Curation
2
3	Use this skill after taxonomy curation and before MAFFT or Agent API submission. The goal is a reproducible accession manifest, not just a broad NCBI query.
4
5	## Workflow
6
7	1. Start from literature/curated accession lists when possible; use broad NCBI queries only as a fallback.
8	2. Record accession, species, genotype/subtype/clade, host, country, date, completeness, length, ambiguous-base fraction, and source.
9	3. Filter by the user’s scope and quality thresholds.
10	4. Deduplicate exact accession and exact sequence hash.
11	5. Keep rejected records and reasons.
12
13	```bash
14	python agentskill/scripts/curate_references.py curate-accessions \
15	--metadata-csv accession_metadata.csv \
16	--taxonomy-json taxonomy.json \
17	--species "Target virus" \
18	--host "target host" \
19	--min-length 1000 \
20	--max-n-fraction 0.05 \
21	--require-complete \
22	--dedupe-by-sequence \
23	--output accession_manifest.json \
24	--accepted-csv accession_accepted.csv \
25	--rejected-csv accession_rejected.csv
26	```
27
28	## Acceptance Gate
29
30	Proceed only when:
31
32	- accepted accessions cover the required groups and time/region scope;
33	- all filters are recorded in `accession_manifest.json`;
34	- rejected records are available for audit;
35	- accession versions are pinned where available.

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6 picks

Type