JBR Genome Browser

JBR Genome Browser is a fast and scalable general purpose genome browser with support of a semi-supervised approach to peak calling.

It supports classic genome browser functionality and provide readily accessible integrated peak annotation and peak calling capabilities. JBR Genome Browser allows researchers to upload tracks of Chip-seq data and perform on-the-fly annotation and peak calling with SPAN algorithm for a given annotation, with the results of peak calling immediately visualized as BED files in the same session.

It can serve not only as an efficient semi-supervised peak calling engine but also as a next-generation genome browser with enhanced functionality for viewing large files, viewing multiple locations simultaneously, and gathering track statistics.

Open Access Paper: https://doi.org/10.1093/bioinformatics/btab376

Citation: Shpynov O, Dievskii A, Chernyatchik R, Tsurinov P, Artyomov MN. Semi-supervised peak calling with SPAN and JBR Genome Browser. Bioinformatics. 2021 May 21.

Features

• Classical genome browser features to visualize various genome data formats
• Supported data file formats: BED (including MACS2, SICER peaks), BigWig, Wig, BigBed, Tdf
• New Supported BAM/SAM/CRAM files including Bisulfite-Sequencing files visualization
• New GTF files support
• Supported session formats: JBR *.yaml, IGV *.xml, UCSC *.txt session files
• Remote URL BigWig/BigBed/BED files support
• New Select tracks by name or wildcard
• New Multiple panels support
• Group scale mode for selected tracks
• Integrated annotation of peaks and on-the-fly semi-supervised peak calling with SPAN
• Enhanced SPAN models visualization
• Support for viewing multiple genomic locations simultaneously
• Optimized for large sessions
• New Detailed track statistics and information on mouse hover
• New BED tracks overlap / Jaccard analysis
• Support for screenshots in PNG or SVG formats
• Headless screenshots done from command line interface
• Support for searching and loading tracks from ENCODE portal
• Easily set up a server using publicly available Docker image
• Full support of High DPI displays
• Genomes configuration editor
• New Mouse mm39, Human hs1 (telomere-to-telomere), hs37-1kg, hs37d5 (decoy genomes)

Note: JBR Genome Browser supports models produced by the SPAN version 2.0+.

Downloads

See releases section for actual information.

See changelog for the latest version here.

Installation

Download a suitable build for your OS from the Downloads section.

• Windows
  Unpack the browser jbr-XXX.zip file.
  Launch jbr.exe.

• MacOS
  

  • For M1+ Mac computers:
    Download the jbr-XXX.dmg macOS Disk Image file
    Mount it as another disk in your system
    Copy JBR Genome Browser to your Applications folder
    If you want to open multiple JBR instances, launch instance with the command:
    open -n "/Applications/JBR.app"
    

  • For Intel-based Mac computers:
    Download the jbr-XXX.jar Java archive file, ensure that you have Java 17+ installed.
    Launch JBR Genome Browser with the command:
    java -jar jbr-XXX.jar"

• Linux:
  Unpack the browser jbr-XXX.tar.gz file using the following command:
  tar -xzf jbr-XXX.tar.gz
  Launch jbr.sh from the bin subfolder.

Web server mode

JBR Genome Browser can be set up as a local web server which allows for an accessible way to share the results. This can be particularly useful when working with private datasets, which cannot be exported to public UCSC browser session, and should be accessible only within local network.
Example of web server mode can be seen at: https://artyomovlab.wustl.edu/jbr/.

Build Docker image or use uploaded to docker.io.

   docker build . -t biolabs/jbr

The user creates a number of preconfigured JRB sessions, place them in a separate <sessions_folder> on the local machine, and easily set up a server using publicly available Docker image biolabs/jbr with the command:

  docker run --publish=5000:5000 --volume=<sessions_folder>:/jbr_sessions --volume=<logs_folder>:/jbr_logs  -d -t biolabs/jbr

Documentation

• Documentation is available in the JBR Wiki on GitHub.
• Semi-supervised peak calling tutorial is available here.

Errors Reporting

Use this Issues Tracker to suggest new features or report bugs.

Authors

JetBrains Research BioLabs homepage