Retrieve nucleotide sequences, raw reads, and genome assemblies from ENA via REST APIs.
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-ena
Please help me install this Agent Skill. Skill: db-ena Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-ena Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-ena
This Skill provides programmatic access to the European Nucleotide Archive (ENA), enabling users to retrieve DNA/RNA sequences, raw reads, and genome assemblies for bioinformatics and genomics pipelines.
Use the db-ena skill to find all samples associated with the ENA study accession PRJEB1234.
High-intent search queries and answers about installing and using this skill.
You can retrieve raw sequencing reads and genome assemblies from the European Nucleotide Archive by querying with specific accession numbers via the Portal API and Browser API. This returns data in formats including FASTQ, FASTA, BAM, and CRAM for bioinformatics pipelines.
Yes, searching ENA studies and samples using taxonomic information and metadata is supported through the Taxonomy REST API. You can query experiments using metadata criteria to find all samples associated with a specific study accession like PRJEB1234.
Accessing nucleotide sequences through the ENA Portal API supports data formats including JSON, TSV, XML, FASTQ, FASTA, BAM, and CRAM. This allows direct integration of retrieved DNA and RNA sequences into bioinformatics workflows.
The best way to programmatically access nucleotide sequences for genomics pipelines is using REST APIs and FTP. This enables automated retrieval of raw reads and genome assemblies by accession number, handling metadata searches for bioinformatics analysis.
No specific dependencies are required to retrieve FASTQ files, as access is handled programmatically through REST APIs and FTP. You can directly query run accessions to download raw sequencing reads without needing additional software libraries.
dotruruQuery ENA data by accession and metadata via Portal and Browser APIs.
tassiovaleAutomate genomic data processing with pysam for SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ files.
sanand0Retrieve nucleotide sequences, FASTQ files, and genome assemblies from ENA via REST APIs.
AvaTar-ArTsRetrieve biological sequences from NCBI and ENA into FASTA or GenBank formats.
