Atb agc

atb agc

Download and inspect genomes in AGC archives

Synopsis

Work with AllTheBacteria genomes distributed as AGC (Assembled Genomes Compressor) archives.

Most users want 'atb agc download': it finds the right archive(s) for an accession or species, downloads them (cache-first, MD5-verified), and extracts FASTA.

The other subcommands are lower-level: 'ls', 'info', and 'get' operate on .agc files you already have on disk; 'install' fetches the upstream agc binary and 'index' builds the by-species index that 'download --species' searches.

Uses the upstream 'agc' binary. Run 'atb agc install' to download it (Linux/macOS x64+arm64, Windows x64).

Options

  -h, --help   help for agc

Options inherited from parent commands

      --config string     config file (default $HOME/.atb/config.toml)
      --data-dir string   directory for the local metadata index (default ~/.local/share/atb/data; override with $ATB_DATA_DIR)

SEE ALSO

• atb - Query and download AllTheBacteria genomes
• atb agc download - Download genome FASTA from AGC archives by accession or species
• atb agc get - Extract sequences as FASTA
• atb agc index - Crawl the OSF node's AGC batches into a searchable TSV index
• atb agc info - Show archive metadata
• atb agc install - Download the agc binary (Linux/macOS x64+arm64, Windows x64)
• atb agc locate - Look up which AGC batch (and OSF part) holds each accession
• atb agc ls - List samples in an archive, or contigs in a sample