BigBacter v1.0
BigBacter is a pipeline aimed at simplifying bacterial genomic surveillance.
This documents BigBacter v1.0, which uses PopPUNK for clustering. If you are running v2.0 or later, see the v2.0 documentation instead — clustering, the database layout, and several parameter names have changed.
Getting Started
- Quick Start — get running with a single species
- Full Instructions — database setup, samplesheets, and pushing results
Reference
- Pipeline Overview — how each stage works
- Inputs — every parameter and what it does
- Outputs — file layout and column descriptions
- Example
BigBacter was originally created by Jared Johnson for the Washington State Department of Health.