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Quick Start

From zero to species identification in 5 to 15 minutes (including databases).

Prerequisites

  • Linux x86_64
  • pixi (manages bioinformatics CLI tools)
  • Python ≥ 3.12

Installation

1. Clone the repository

git clone https://github.com/indexofire/gside.git
cd gside

2. Bioinformatics tools

pixi install

Automatically fetches blast, skani, mash, sourmash, etc.

3. Python package

pip install -e .

4. Verify

gside --version
gside db status     # markers should be ✅

Databases

gside uses a tiered database design:

Tier Contents Size Status
mini Marker rules + sequences ~1MB ✅ Bundled with repo
panel Curated reference panel (skani sketch) ~130MB Requires gside db setup
mash RefSeq MinHash sketch ~179MB Requires gside db setup
all panel + mash ~310MB One-time install

The marker mode works out of the box with the bundled mini tier. The panel, mash_refseq, and all modes need a one-time database download:

gside db setup --tier all

See Databases for details.

Next Steps