Does this skill help with ENA API rate limits?

Yes, it provides best practices for managing the 50 requests per second limit, including exponential backoff and batching strategies.

Which file formats are supported for sequence data?

The skill facilitates access to various formats including FASTQ, BAM/CRAM, FASTA, and EMBL flat file formats.

Can I search for data by organism name?

Yes, the skill supports querying the ENA Taxonomy REST API to find records based on organism names, lineage, or taxon IDs.

What data can I retrieve with the ENA Database skill?

You can retrieve raw reads (FASTQ), genome assemblies, DNA/RNA sequences, study metadata, sample information, and taxonomic records.

How are bulk downloads handled?

For large datasets, the skill provides guidance on using FTP, Aspera, or the enaBrowserTools command-line utility for efficient transfer.

ENA Database Explorer

Name: ENA Database Explorer
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Interfaces with the European Nucleotide Archive to retrieve genomic sequences, raw reads, and metadata for bioinformatics workflows.

The ENA Database skill provides a specialized interface for interacting with the European Nucleotide Archive (ENA), a massive public repository for nucleotide sequence data. It allows users to programmatically query and download DNA/RNA sequences, raw reads (FASTQ), genome assemblies, and associated metadata through various REST APIs and FTP protocols. Ideal for bioinformatics and genomics pipelines, this skill streamlines data discovery across studies, samples, and experiments while managing technical details like rate limiting, complex API parameters, and hierarchical data structures.

Key Features

01Taxonomic data and lineage querying for specific organisms

020 GitHub stars

03Programmatic retrieval of raw sequencing reads and FASTQ files

04Advanced metadata search via the ENA Portal and Browser APIs

05Genome assembly discovery and bulk download guidance

06Cross-reference searching with external biological databases

Use Cases

01Automating the discovery of all sequencing samples within a project

02Fetching specific genome assemblies for comparative genomic analysis

03Integrating ENA data retrieval into high-throughput bioinformatics pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos ena-database

For use in Claude.ai and ChatGPT

Download Skill