BGB 2.0 – BaseClear Genome Browser

BGB 2.0

:: DESCRIPTION

The BGB is a graphical software application to view and compare differences multiple genomes. It’s main application is in the area of Next Generation Sequencing (NGS) experiments where the tool allows easy comparison of mutation data across multiple samples.

::DEVELOPER

BaseClear B.V.

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BGB

:: MORE INFORMATION

cis-Browser 1.0 – Genome Browser for Cis-regulatory Information

cis-Browser 1.0

:: DESCRIPTION

cis-Browser (cis-Regulatory Browser) is genome browser for cis-regulatory information inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation

::DEVELOPER

The Istrail Laboratory of Brown University

:: SCREENSHOTS

cis-Browser

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 cis-Browser

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;674:369-99. doi: 10.1007/978-1-60761-854-6_22.
Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks.
Istrail S, Tarpine R, Schutter K, Aguiar D.

ChromoZoom – web-based Genome Browser

ChromoZoom

:: DESCRIPTION

ChromoZoom is a web-based genome browser currently hosting tracks for the yeast and human genomes.

::DEVELOPER

Roth Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Ruby
  • rake

:: DOWNLOAD

 ChromoZoom

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 1;29(3):384-6. doi: 10.1093/bioinformatics/bts695. Epub 2012 Dec 6.
ChromoZoom: a flexible, fluid, web-based genome browser.
Pak TR, Roth FP.

UTGB Toolkit 1.5.8 – Personalized Genome Browser

UTGB Toolkit 1.5.8

:: DESCRIPTION

UTGB Toolkit (University of Tokyo Genome Browser)  is an open-source software for developing personalized genome browsers that work in web browsers.

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 UTGB Toolkit

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Aug 1;25(15):1856-61. Epub 2009 Jun 3.
UTGB toolkit for personalized genome browsers.
Saito TL, Yoshimura J, Sasaki S, Ahsan B, Sasaki A, Kuroshu R, Morishita S.

 

BQGB 090528 – Berkeley Quantitative Genome Browser

BQGB 090528

:: DESCRIPTION

BQGB (Berkeley Quantitative Genome Browser, sometimes known as “bbrowse”, “bbrowser”) duplicates much of the annotation display functionality typical of a genome browser but with an emphasis on custom and quantitative data such as that produced in high throughput sequencing and genome-wide association studies. The application runs locally on a user’s desktop or laptop computer, avoiding the slow back-and-forth of web based genome browsers. BQGB expects data files to be local to the application process and in a file format such as GFF, BED, SGR, WIG, FASTA or any column delimited format that provides sequence and base pair position locations. This topography should generally be faster than that of a central remote database plus web based browser when working with many custom files, ie. downloading a single reference annotation to one’s local machine is quicker than uploading hundreds of custom data files to a remote server!

::DEVELOPER

Berkeley Drosophila Transcription Network Project

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • QT
  • GCC

:: DOWNLOAD

BQGB

:: MORE INFORMATION

License

Argo 2 – Genome Browser

Argo 2

:: DESCRIPTION

Argo is a production tool for visualizing and manually annotating whole genomes.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Argo (This version won’t work unless you have Broad VPN access. If you are collaborating with a Principle Investigator at the Broad, please ask that person about getting an Argo user account.)

:: MORE INFORMATION