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thanhleviet merged 1 commit into from
Jul 4, 2026
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docs(agc): note command group ships in v0.18.0 #32

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3 changes: 3 additions & 0 deletions docs/guides/agc.md
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Expand Up @@ -7,6 +7,9 @@ AllTheBacteria assemblies are distributed as **AGC** (Assembled Genome Compresso
- **`atb agc index`** — build a searchable index of the OSF-hosted archives (what `--species` searches).
- **`atb agc install`** — fetch the upstream `agc` binary the others shell out to.

!!! info "Availability"
The `atb agc` command group is new in **v0.18.0**; it is not in v0.17.x. The 0.18.0 line is currently in beta while the by-species workflow settles, so install it from the [v0.18.0-beta.2 pre-release](https://github.com/AllTheBacteria/atb-cli/releases/tag/v0.18.0-beta.2) (newer betas appear on the [releases page](https://github.com/AllTheBacteria/atb-cli/releases)). The installer's default stays on the latest stable until 0.18.0 is released.

!!! note "Which command do I want?"
Reach for **`atb agc download`** to get genomes by sample accession or by species — it handles resolution, download, and extraction. Drop down to **`atb agc ls`/`info`/`get`** only when you already have a local `.agc` file, or to **`atb agc index`** when you want to (re)generate the by-species index. All shell out to the upstream `agc` binary, so install it first.

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