GEOfastq

GEOfastq downloads FASTQ files from the European Nucleotide Archive (ENA) using Gene Expression Omnibus (GEO) accessions.

Key Features:

• GEO Accession Input: Accepts GEO accessions as the starting point for retrieving sequencing data.
• Metadata Retrieval: Retrieves sample metadata from GEO and the Sequence Read Archive (SRA).
• FTP Link Construction: Constructs FTP download links for FASTQ files hosted by the ENA.
• Aspera Link Construction: Constructs Aspera download links for FASTQ files hosted by the ENA.
• SRA Run Accession Mapping: Uses SRA run accessions to map GEO entries to ENA FASTQ files.

Scientific Applications:

• RNA-seq Data Acquisition: Facilitates retrieval of FASTQ files for gene expression analysis studies deposited in GEO.
• High-throughput Sequencing Data Access: Enables streamlined access to ENA-hosted sequencing data without direct ENA accession knowledge.
• Cross-database Data Integration: Bridges GEO, SRA, and ENA databases to locate and download raw sequencing reads.

Methodology:

GEOfastq retrieves sample metadata from GEO and SRA, then uses SRA run accessions to construct FTP and Aspera download links for FASTQ files generated by the ENA.