Research group

BioLabs

JBR Genome Browser

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

One of the major challenges of semi-supervised learning is the procedural complexity of manual data annotation, which often leads to inaccuracies and mix-ups. We created a brand new visualization tool that would support 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 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. It provides enhanced functionality for viewing large files, viewing multiple locations simultaneously, and gathering track statistics.

Contents

Features

  • On-the-fly peak calling using SPAN models
  • Integrated annotation of peaks for semi-supervised peak calling
  • Support for viewing multiple genomic locations simultaneously
  • Classical genome browser features to visualize various genome data formats
  • Supported data file formats: BED (including MACS2, SICER peaks), BigWig, Wig, BigBed, Tdf
  • Supported session formats: JBR *.yaml, IGV *.xml session files
  • Remote URL BigWig/BigBed/BED files support
  • Show track statistics
  • BED tracks overlap analysis
  • Optimized for large sessions
  • Support for screenshots in PNG or SVG formats
  • New Support for searching and loading tracks from ENCODE portal
  • New Server mode visualizing single or multiple sessions in a web browser
    See an example at https://artyomovlab.wustl.edu/jbr/
  • New Full support of High DPI displays

NOTE: JBR Genome Browser 1.0.beta.5244 supports models produced by the SPAN version 0.12+

System Requirements

  • Operating System:
    • Microsoft Windows 10/8/7
    • MacOS 10.8 or higher
    • Linux. Recommended desktops: GNOME, KDE or UNITY
  • 2 GB RAM minimum
  • 1024x768 minimum screen resolution

Downloads

Download Description
jbr-1.0.beta.5244.zip Windows archive (includes bundled 64-bit Java Runtime)
jbr-1.0.beta.5244.dmg Mac installer (includes bundled 64-bit Java Runtime)
jbr-1.0.beta.5244.tar.gz Linux archive (includes bundled 64-bit Java Runtime)

Installation

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

Windows:

  • Unpack the browser 1.0.beta.5244.zip file:
  • Run jbr.exe.

MacOS:

  • Download the 1.0.beta.5244.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 a second, third, etc. instances using the command:
open -n "/Applications/JBR 1.0.app"

Linux:

  • Unpack the browser 1.0.beta.5244.tar.gz file using the following command: 
    tar -xzf 1.0.beta.5244.tar.gz
  • Run jbr.sh from the bin subfolder.

Documentation

General

See the JBR Wiki on GitHub.

Visual Peak Calling Tutorial

Comprehensive step-by-step tutorial on using integrated peak calling solution is available in the How-To section.

Errors Reporting

Report any errors or comments in the public JBR Genome browser issue tracker.

Modified Wed Aug 12 17:19:12 2020 UTC