What biological data formats does this skill support?

The skill facilitates the retrieval of metadata in XML, JSON, and TSV, as well as biological data in FASTQ, FASTA, BAM/CRAM, and EMBL flat file formats.

Can I use this skill for bulk data downloads?

Yes, the skill provides implementation patterns for identifying accessions via the Portal API and then utilizing FTP or Aspera for high-speed bulk transfers.

Does the ENA API have rate limits?

Yes, ENA APIs generally have a limit of 50 requests per second. This skill includes best practices for exponential backoff and rate limit handling.

How do I search for sequences by organism?

You can use the integrated Taxonomy REST API or search the Portal API using taxonomic IDs or tree-based queries to find data for specific species.

ENA Database Access

Name: ENA Database Access
Author: pur3v4d3r

bypur3v4d3r

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데이터 과학 및 ML

Accesses and retrieves nucleotide sequences, raw reads, and genome assemblies from the European Nucleotide Archive for bioinformatics workflows.

This skill empowers Claude to interact with the European Nucleotide Archive (ENA), a premier global repository for DNA and RNA sequence data. It provides standardized methods for querying the ENA Portal and Browser APIs, enabling researchers and developers to programmatically search for studies, samples, and sequencing runs. By streamlining the retrieval of FASTQ files, assemblies, and taxonomic metadata, this skill facilitates the direct integration of high-throughput sequencing data into bioinformatics pipelines and computational biology projects.

주요 기능

01Programmatic access to ENA Portal and Browser REST APIs

02Automated retrieval of raw sequencing reads and genome assemblies

03Comprehensive taxonomic information and lineage lookups

04Support for multiple data formats including XML, JSON, FASTQ, and FASTA

05Implementation patterns for bulk data transfer via FTP and Aspera

061 GitHub stars

사용 사례

01Automating the retrieval of sequencing data for specific study accessions

02Querying genomic metadata to build custom bioinformatics datasets

03Integrating taxonomic and functional annotation data into analysis pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add pur3v4d3r/pur3-pkb-codebase ena-database

For use in Claude.ai and ChatGPT

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