GEO Getter

Download raw FASTQ files linked to public GEO / ENA records, plus supplementary and processed files distributed through GEO.

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Data types

• Raw FASTQ files associated with public SRA / ENA / DRA accessions.
• Supplementary and processed files distributed through GEO records.

Install

Download the latest GEO Getter release from GitHub Releases.

• For most users, download the .exe installer and start GEO Getter from the Start menu.
• For a no-install setup, download the win-x64-portable.zip archive, extract it, and run start_geo_getter.vbs.
• Requirements: Windows 10 or 11, 64-bit; internet access; and enough free disk space for the files you choose.
• The installer is unsigned, so Windows SmartScreen may display a warning.

Quick start

1. Start GEO Getter.
2. Paste a supported accession or GEO page URL.
3. Select Find files.
4. Select the raw FASTQ, supplementary, or processed files to download.
5. Confirm the output folder. By default, GEO Getter creates an accession folder under Downloads\GEOGetter.
6. Select Download selected files.

Supported input

Input	Examples
GEO accession	GSE52778, GSM...
GEO page URL	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52778
SRA / ENA / DRA accession	SRP..., SRX..., SRR..., SRS..., ERP..., ERX..., ERR..., ERS..., DRP..., DRX..., DRR..., DRS...
BioProject accession	PRJNA..., PRJEB..., PRJDB...
BioSample accession	SAMN..., SAMEA..., SAMD...

Output folder

Downloaded files, TSV manifests, and logs are written to the accession folder shown in the app.

Downloads/GEOGetter/
  GSE52778/
    GSE52778_fastq_manifest.tsv
    GSE52778_supplementary_manifest.tsv
    GSE52778_download_log.tsv
    SRR1039508_1.fastq.gz

• *_fastq_manifest.tsv: FASTQ source URL, ENA MD5 when available, expected size, and output path.
• *_supplementary_manifest.tsv: GEO supplementary or processed file URL and output path.
• *_download_log.tsv: download result for each selected file.
• verification_report.tsv: report produced by a later FASTQ verification run.

Verification and resume

• FASTQ files are checked against ENA MD5 values when ENA provides them.
• GEO supplementary and processed files are downloaded from GEO URLs; they are not checked against ENA FASTQ MD5 values.
• To verify downloaded FASTQ files later, choose Tools > Verify saved FASTQ and select a *_fastq_manifest.tsv file. GEO Getter writes verification_report.tsv in the same folder.
• To resume an interrupted FASTQ download, choose the same save folder. Resume works only when the existing FASTQ manifest and download log in that folder match the current FASTQ selection. Incomplete files remain as .part files.