Retrieve ENA sequences, reads, and assemblies via REST APIs and FTP.
npx skills add https://github.com/m0at/claudemd --skill ena-database-m0at
Please help me install this Agent Skill. Skill: ena-database Source: https://github.com/m0at/claudemd/tree/main/skills/ena-database Command: npx skills add https://github.com/m0at/claudemd --skill ena-database-m0at
The ENA Database Skill enables programmatic access to nucleotide data from the European Nucleotide Archive (ENA) via REST APIs and FTP, simplifying retrieval of sequences, raw reads, and genome assemblies for genomics pipelines.
Query ENA by accession to fetch sequences or reads and download data via FTP or Aspera.
High-intent search queries and answers about installing and using this skill.
Retrieve sequences and raw reads from ENA by querying accession numbers via the Portal API or Browser API. You can fetch studies, samples, assemblies, and analyses programmatically, exporting results in JSON, TSV, CSV, or XML formats for downstream genomics workflows.
The best way to bulk download nucleotide sequences is via the ENA FTP or Aspera services. This approach enables scalable data retrieval of raw reads and assemblies, satisfying bulk download requirements for large-scale genomics pipelines without individual record fetching.
Yes, you can get taxonomy and cross-reference information for ENA samples programmatically. The Taxonomy REST API and Cross-Reference services allow you to integrate ENA nucleotide data with external resources, enabling cross-reference lookups for studies, samples, and assemblies.
Yes, the ENA API supports exporting search results in FASTA and FASTQ formats. In addition to JSON, TSV, CSV, and XML, you can download raw reads and sequences directly in these standard genomics formats for immediate use in bioinformatics pipelines.
Search ENA studies and samples by metadata using the Portal API, which supports scalable querying based on sample attributes and study descriptions rather than specific accession numbers. This allows flexible discovery of assemblies and raw reads matching your research criteria.
Limitations of using REST APIs for ENA data retrieval include potential rate limits and overhead for very large datasets, where FTP or Aspera bulk downloads are more efficient. API queries are best for metadata searching and cross-reference lookups rather than massive raw read downloads.
sanand0Retrieve nucleotide sequences, FASTQ files, and genome assemblies from ENA via REST APIs.
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jimmc414Retrieve nucleotide sequences, FASTQ reads, and genome assemblies from ENA via REST APIs and FTP.
