# Biofilter Documentation

Lightweight, user-focused documentation for running Biofilter today.

This documentation is intentionally practical:
- install/configure quickly (PyPI, source, or Docker)
- bootstrap database and run ETL
- run reports via CLI/API
- troubleshoot common operational issues

```{toctree}
:maxdepth: 2
:caption: Getting Started

getting_started/index
getting_started/installing
getting_started/connecting_db
getting_started/finding_reports
getting_started/running_reports
```

```{toctree}
:maxdepth: 2
:caption: Reference

system_overview
entity_and_omics
developer_extensions
configuration
database
schema
etl
reports
report_catalog
cli_reference
troubleshooting
```