Introduction - Config guide

The following guide provides comprehensive information regarding the anatomy and usage of the config.json file that is critical for running a JBrowse 2 session.

Getting started#

• Intro to the config.json format - Overall structure and key fields of the config.json file

Core configuration#

• Configuring assemblies - Setting up reference genomes with sequence adapters and refname aliases
• Configuring plugins - Adding first- and third-party plugins via config.json
• Configuring tracks - Configuration options common to all track types

Track types#

• Alignments track configuration - BAM/CRAM track config with BamAdapter and CramAdapter options
• Hi-C track configuration - Contact matrix track config using the HicAdapter
• Multi-quantitative tracks - Multiple BigWig/BedGraph signals combined into one display
• Quantitative tracks - BigWig/BedGraph signal track config and display options
• Synteny track config - Synteny track config for dotplot and linear synteny views
• Variant track configuration - VCF variant track config and breakpoint split view options

Callbacks and customization#

• Customizing feature colors with callbacks and plugins - Per-feature color callbacks using jexl or plugin code
• Customizing feature details with callbacks and plugins - Customizing feature detail panels with the formatDetails slot
• FromConfig adapters - Inline data adapters for embedding small datasets directly in config
• Using jexl callbacks - Dynamic configuration using jexl callback expressions

Other features#

• Avoiding stale config - Cache-busting strategies for servers that aggressively cache config.json
• Default session - Setting an initial session state loaded for all users
• Disabling analytics - Opt out of Google Analytics usage tracking
• Text searching - Per-track and aggregate full-text search indexes
• Coloring/theming - Customizing the application color theme
• Hierarchical track selector - Track grouping and display options for the hierarchical selector