Query ENA nucleotide data and metadata via REST APIs and FTP.
npx skills add https://github.com/OwnLabAI/ownlab --skill ena-database-ownlabai
Please help me install this Agent Skill. Skill: ena-database Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/ena-database Command: npx skills add https://github.com/OwnLabAI/ownlab --skill ena-database-ownlabai
Access and integrate ENA nucleotide sequence data and metadata via REST APIs and FTP for genomics workflows.
Query ENA Portal API to fetch sample records by study_accession and download related FASTQ files.
High-intent search queries and answers about installing and using this skill.
To retrieve ENA nucleotide sequences and metadata, you can query accession or study identifiers via the REST Portal API and Browser API. This returns records in JSON, TSV, or XML formats to integrate directly into genomics pipelines.
Yes, you can bulk download raw reads, assemblies, and sequences from the ENA database using FTP or Aspera. This supports large-scale data retrieval for high-throughput genomics workflows.
The ENA Portal API supports multiple response formats for sequence data retrieval, including JSON, TSV, and XML. FASTQ and FASTA files are also supported for downloading raw reads and assemblies.
Yes, the ENA REST API provides taxonomy and cross-reference data by accession. It integrates the Taxonomy REST API and xref services to retrieve taxon data and cross-references for studies, samples, and runs.
The best way to fetch sample records by study accession and download FASTQ files is querying the ENA Portal API. You retrieve the sample metadata in JSON or TSV, then use the returned accessions to download FASTQ files via FTP or Aspera.
The ENA Browser API and Portal API differ in scope for data retrieval. The Portal API searches studies, samples, and assemblies comprehensively, while the Browser API provides specific record views, so Portal API is preferred for broad pipeline integration.
ovachieverRetrieve nucleotide sequences and associated data from ENA via REST APIs.
Mathews-TomSearch YouTube with yt-dlp and return structured video metadata.
silversteinRetrieve nucleotide sequences and raw reads from the ENA via APIs and FTP/Aspera workflows.
AvaTar-ArTsRetrieve biological sequences from NCBI and ENA into FASTA or GenBank formats.
