ena-database
Retrieve ENA Genomics Data
Researchers need reliable ENA queries and downloads. This skill guides Claude, Codex, and Claude Code through ENA APIs, formats, accessions, and bulk retrieval choices.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "ena-database" from https://skillstore.io/skills/davila7-ena-database.md and its manifest at https://skillstore.io/api/skills/davila7-ena-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "ena-database". Find samples from a study accession and choose useful metadata fields.
Expected outcome:
- Use the Portal API search endpoint with the sample result type.
- Filter by the study accession and request accession, title, collection date, and scientific name fields.
- Use TSV for spreadsheet review or JSON for automated processing.
Using "ena-database". Retrieve a sequence record in FASTA format.
Expected outcome:
- Use the Browser API FASTA endpoint for the sequence accession.
- Add a range only when a subsequence is needed.
- Check the response status and keep the accession in your citation notes.
Using "ena-database". Download many FASTQ files for downstream analysis.
Expected outcome:
- First request file report metadata with FASTQ links, sizes, and checksums.
- Use a bulk transfer method for large datasets and verify checksums after download.
- Respect ENA rate limits when using repeated API requests.
Security Audit
SafeThe skill is documentation-focused and its network examples target official public ENA and EBI services. Most static findings are false positives from Markdown examples, but the FTP download guidance is a real medium-risk transport issue because it uses unencrypted ftp:// URLs.
Capability review items (2)
These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.
Risk Factors
🌐 Network access (48)
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<iframe src="https://skillstore.io/embed/skills/davila7-ena-database.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
davila7. (2026). ena-database security audit report (audit version 15) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-ena-database/audits/15BibTeX citation
@techreport{davila7-davila7-ena-database-2026,
author = {davila7},
title = {ena-database security audit report (audit version 15)},
institution = {Skillstore},
year = {2026},
number = {15},
url = {https://skillstore.io/skills/davila7-ena-database/audits/15},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "ena-database security audit report (audit version 15)"
version: "unspecified"
type: report
authors:
- name: "davila7"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/davila7-ena-database/audits/15"
identifiers:
- type: other
value: "skillstore:davila7-ena-database:audit:15"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
davila7-ena-database
2026-08-21
k-dense-ai-ena-database
2026-08-21
Skillstore Score
Why this score Evidence Confidence: HighWhat You Can Build
Find sequencing runs for a study
Plan an ENA Portal API query that lists runs, metadata fields, FASTQ links, and checksums for one study accession.
Retrieve sequence records by accession
Choose the right Browser API endpoint and output format for FASTA, XML metadata, or EMBL flat files.
Prepare bulk download workflows
Compare API, FTP, Aspera, and enaBrowserTools options before downloading large read or assembly datasets.
Try These Prompts
Use the ena-database skill to tell me which ENA endpoint and output format I should use for accession ERR123456. Explain the expected result.
Use the ena-database skill to design a Portal API search for RNA-Seq experiments in study PRJNA123456. Include result type, fields, filters, and format.
Use the ena-database skill to plan how to retrieve FASTQ URLs and checksums for all runs in PRJEB1234. Include pagination, rate limiting, and validation steps.
Use the ena-database skill to review my ENA bulk download approach for a metagenomics project. Compare API, Aspera, FTP, and enaBrowserTools tradeoffs.
Best Practices
- Start with narrow result types and only request fields needed for the analysis.
- Use pagination, retry handling, and delays to stay within ENA rate limits.
- Record study, sample, run, and assembly accessions for reproducibility and citation.
Avoid
- Do not loop through large accession lists without delays or retry handling.
- Do not parse XML or FASTA with fragile regular expressions.
- Do not download large datasets without checking sizes, storage, and checksums first.
Frequently Asked Questions
What is the ENA database?
Can this skill download data directly?
Which formats does the skill cover?
Does it support taxonomy lookup?
How should I handle large datasets?
Is this useful in Claude Code and Codex?
Developer Details
Author
davila7License
MIT
Skillstore revision
r1
Version notice
The author did not declare a version.
Ref
b959ebfd1043a07c0c4378ab94ca4342cb0259f5
Maintenance freshness
7/20/2026
Usage
6 downloads · 576 views
File structure