What is the ENA Database skill for Claude?

It is a specialized skill that allows Claude to search, query, and retrieve genomic data from the European Nucleotide Archive using its REST APIs and FTP services.

Can I download raw sequencing reads with this skill?

Yes, the skill provides patterns for identifying and retrieving raw sequencing reads (FASTQ) and genome assemblies using accession numbers.

Does the skill handle ENA API rate limits?

Yes, it includes guidance on managing ENA's 50 requests per second limit, including implementation patterns for exponential backoff and batching.

What data formats are supported?

The skill supports metadata in XML, JSON, and TSV/CSV, as well as sequence data in FASTQ, FASTA, BAM/CRAM, and EMBL flat file formats.

How do I perform bulk downloads using this skill?

The skill facilitates bulk downloading by helping you extract file URLs via the Portal API and providing instructions for high-speed transfers via FTP or Aspera.

ENA Database Access

Name: ENA Database Access
Author: lifangda

bylifangda

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데이터 과학 및 ML

Accesses the European Nucleotide Archive to retrieve genomic sequences, raw reads, and metadata for bioinformatics pipelines.

소개

The ENA Database skill enables Claude to programmatically interact with the European Nucleotide Archive (ENA), a leading public repository for nucleotide sequence data. It provides streamlined access to DNA/RNA sequences, raw sequencing reads, and comprehensive genome assemblies through REST APIs and FTP. This skill is essential for bioinformatics workflows, allowing researchers and developers to query metadata, search across studies and samples, and automate the retrieval of FASTQ or FASTA files directly within their coding environment.

주요 기능

Search and access genome assemblies at various completion levels
16 GitHub stars
Query metadata for studies, samples, and experiments via ENA Portal API
Support for multiple formats including FASTQ, FASTA, XML, and JSON
Retrieve DNA/RNA sequences and raw reads by accession number
Access taxonomic information and lineage data for organisms

사용 사례

Searching for and downloading public datasets based on metadata criteria
Integrating ENA cross-references into bioinformatics software tools
Automating the retrieval of sequencing data for secondary analysis pipelines

소개

주요 기능

Search and access genome assemblies at various completion levels
16 GitHub stars
Query metadata for studies, samples, and experiments via ENA Portal API
Support for multiple formats including FASTQ, FASTA, XML, and JSON
Retrieve DNA/RNA sequences and raw reads by accession number
Access taxonomic information and lineage data for organisms

사용 사례

Searching for and downloading public datasets based on metadata criteria
Integrating ENA cross-references into bioinformatics software tools
Automating the retrieval of sequencing data for secondary analysis pipelines