Transfer Services (FTP) file server

How to download data from MGnify’s file server

Author

Affiliation

Published

June 2, 2026

Transfer Services

EMBL-EBI operates a Transfer Services file server, providing high-bandwidth access to datasets from EMBL-EBI services including MGnify.

MGnify’s (public) results are available in the following directories:

Metagenomic analyses (i.e. the files produced when analysing MGYA-accessioned analyses) from https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_results/
- These files are arranged into directories using the studies’ INSDC acccessions, with substring-prefixed folder names, and then their MGnify Pipeline version number. E.g. the version 5.0 analysis of ERP003408 is found in ERP003/ERP003408/version_5.0.
Genomes (i.e. the files produced when analysing MGYG-accessioned genomes from catalogues) from https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/
- These files are arranged into the biome-specific catalogues according to the MGnify Genomes schema
Proteins (the MGnify Protein database of proteins found in metagenome assemblies) from https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/
- These files are arranged into date-versioned releases. The latest release is always linked from https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/current_release/

Citation

BibTeX citation:

@online{2026,
  author = {, MGnify},
  title = {Transfer {Services} {(FTP)} File Server},
  date = {2026-06-02},
  url = {https://docs.mgnify.org/src/docs/ftp.html},
  langid = {en}
}

For attribution, please cite this work as:

MGnify. 2026. “Transfer Services (FTP) File Server.” June 2. https://docs.mgnify.org/src/docs/ftp.html.