Browsing OSF files

The AllTheBacteria project hosts ~3,000 files on OSF across 75+ categories (assemblies, annotations, AMR, MLST, protein structures, and more). Use atb osf to browse and download them directly.

Browse and download

# List all project categories
atb osf ls

# Find files matching a keyword
atb osf ls AMR
atb osf ls "Protein Structures"

# Regex search across project and filename
atb osf ls --grep "bakta.*batch"

# Sort by size, different output formats
atb osf ls AMR --sort size --format json

# Preview what would be downloaded
atb osf download --dry-run "AMRFinderPlus.*results.*latest"

# Download with MD5 verification
atb osf download --verify "DefenseFinder.*results"

# Download all files in a project
atb osf download --project AllTheBacteria/MLST --all -o ./mlst_data

Extract assembly tarballs

The .tar.xz batches contain uncompressed FASTA files; --extract unpacks them, --compress chooses the on-disk encoding (none, gz (default), or xz), and --delete-archive removes each tarball once it has extracted successfully:

# Download all assembly batches and extract FASTAs as .fa.gz, removing tarballs
atb osf download --project AllTheBacteria/Assembly --all \
    --extract --compress gz --delete-archive -o ./assemblies

# One batch, raw FASTA, keep the tarball
atb osf download "Assembly.*batch.*1\." --extract --compress none

The file index is cached locally and refreshed every 7 days. Use --refresh to force an update.