# Config guide

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How to write the assemblies, tracks and settings a JBrowse session is built
from. They are the same objects in a served `config.json`, in a `jbrowse` CLI
command, and pasted into a running JBrowse Web or Desktop, so a guide here
applies wherever you run it. For copy-paste recipes, see the [Cookbook](https://jbrowse.org/jb2/docs/cookbook).

## Core configuration

- [config.json format](https://jbrowse.org/jb2/docs/config_guides/intro)
- [Assemblies](https://jbrowse.org/jb2/docs/config_guides/assemblies)
- [Tracks](https://jbrowse.org/jb2/docs/config_guides/tracks)
- [Authentication](https://jbrowse.org/jb2/docs/config_guides/authentication)
- [Config slot types](https://jbrowse.org/jb2/docs/config_guides/slot_types)
- [Connections](https://jbrowse.org/jb2/docs/config_guides/connections)
- [FromConfig adapters](https://jbrowse.org/jb2/docs/config_guides/from_config)
- [Plugins](https://jbrowse.org/jb2/docs/config_guides/plugins)
- [Supported file types](https://jbrowse.org/jb2/docs/config_guides/file_types)
- [Text searching](https://jbrowse.org/jb2/docs/config_guides/text_searching)

## Track types

- [Alignments track](https://jbrowse.org/jb2/docs/config_guides/alignments_track)
- [Grouping and lane order](https://jbrowse.org/jb2/docs/config_guides/grouping_and_ordering)
- [GWAS track](https://jbrowse.org/jb2/docs/config_guides/gwas_track)
- [Hi-C track](https://jbrowse.org/jb2/docs/config_guides/hic_track)
- [MAF track](https://jbrowse.org/jb2/docs/config_guides/maf_track)
- [Mark display](https://jbrowse.org/jb2/docs/config_guides/mark_display)
- [Mark display examples](https://jbrowse.org/jb2/docs/config_guides/mark_display_examples)
- [Quantitative track](https://jbrowse.org/jb2/docs/config_guides/quantitative_track)
- [Synteny track](https://jbrowse.org/jb2/docs/config_guides/synteny_track)
- [Variant track](https://jbrowse.org/jb2/docs/config_guides/variant_track)

## Callbacks

- [Customizing feature colors](https://jbrowse.org/jb2/docs/config_guides/customizing_feature_colors)
- [Customizing feature details](https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details)
- [Using jexl callbacks](https://jbrowse.org/jb2/docs/config_guides/jexl)

## Appearance

- [Coloring/theming](https://jbrowse.org/jb2/docs/config_guides/theme)
- [Default session](https://jbrowse.org/jb2/docs/config_guides/default_session)
- [Hierarchical track selector](https://jbrowse.org/jb2/docs/config_guides/track_selector)

## Deployment

- [Avoiding stale config](https://jbrowse.org/jb2/docs/config_guides/avoiding_stale_config)
- [Deploying JBrowse Web](https://jbrowse.org/jb2/docs/config_guides/deploying)
- [Disabling analytics](https://jbrowse.org/jb2/docs/config_guides/disable_analytics)
- [Serving data files](https://jbrowse.org/jb2/docs/config_guides/serving_data)