ena-database

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

1.15x

Quality

70%

Does it follow best practices?

Impact

96%

1.15x

Average score across 3 eval scenarios

Securityby

Advisory

Suggest reviewing before use

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/ena-database/SKILL.md

Evaluation results

89%

21%

RNA-Seq Experiment Catalog for Arabidopsis thaliana

Portal API metadata search with pagination and rate limiting

Criteria

Without context

With context

Portal API endpoint

100%

tax_tree query syntax

100%

RNA-Seq filter in query

100%

TSV or JSON format

100%

Fields limiting

100%

Pagination implemented

50%

HTTP status check

100%

Rate limit handling

100%

Output file format

71%

85%

requests.Session usage

100%

No XML parsing

100%

Script runs successfully

70%

50%

100%

14%

FASTQ Download Manifest Generator

File report retrieval with retry session and FTP URL extraction

Criteria

Without context

With context

filereport endpoint

100%

result=read_run parameter

100%

fastq_ftp field requested

100%

fastq_md5 field requested

100%

fastq_bytes field requested

100%

Session with Retry adapter

33%

100%

Retry on 429 and 5xx

50%

100%

HTTP status check

100%

No file downloads

100%

TSV or JSON output format

100%

Output file created

83%

100%

Organism Taxonomy and Sample Metadata Reporter

Taxonomy lookup with caching and XML parsing via proper library

Criteria

Without context

With context

Taxonomy REST API endpoint

100%

Taxonomy caching implemented

100%

taxonomy_cache.json written

100%

Browser API XML retrieval

100%

Proper XML library import

100%

Portal API for sample discovery

100%

HTTP status check

57%

100%

lineage field populated

100%

TSV output created

100%

No regex XML parsing

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: 71add64

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

RNA-Seq Experiment Catalog for Arabidopsis thaliana FASTQ Download Manifest Generator Organism Taxonomy and Sample Metadata Reporter

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