Genomizer

Genomizer is a platform independent Java program for the analysis of genome wide association experiments.

Genomizer is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. Genomizer is not for commercial use.

For haplotype analysis, Genomizer uses whap (Shaun Purcell/Pak Sham). Instructions and source code can be found here.

When using please cite the following publication:
Franke A, Wollstein A, Teuber M, Wittig M, Lu T, Hoffmann K, Nurnberg P, Krawczak M, Schreiber S, Hampe J (2006).
GENOMIZER: an integrated analysis system for genome-wide association data.
Human Mutat 27(6):583-588
PubMed (PMID:16652332)


System Requirements
Installation Instructions
Download
Screenshots

 


System Requirements

Genomizer runs on all Windows and Linux platforms.

 


Installation Instructions

Before you run the Genomizer setup program you need to install a Java Runtime Environment and a MySQL database server on your computer. Both installations are straightforward and do not require any advanced computer skills.

  • Java
    Because Genomizer is written in Java you need a Java platform (including Java virtual machine) on your computer in order to run the program. Make sure you have version 1.4 or higher of the Java 2 Runtime Environment (J2RE) Standard Edition from Sun installed on your system. Overwriting existing J2RE installations might cause problems with other installed programs.

    downloads: https://java.sun.com/downloads/index.html
    homepage: https://java.sun.com



     
  • MySQL
    You need to have a MySQL database server running on your computer. Version 4.0 or higher is recommended. After having installed MySQL you must create a new database called "genomizer". You can do this with the included command line client by typing the SQL command 'create database genomizer'. Alternatively you can use a graphical client (see the MySQL website for recommended programs). The required tables can later be created with Genomizer. Instead of using a local database server you might connect to a remote server over the network.

    downloads: https://dev.mysql.com/downloads
    homepage: https://www.mysql.com


After having installed the Java 2 Runtime Environment and MySQL you can run the Genomizer installer.

To view the graphical output of Genomizer on Windows computers you need to install Adobe SVG Viewer.
downloads: https://www.adobe.com/svg/viewer/install/
homepage: https://www.adobe.com



For viewing SVG under Linux we recommend to use Squiggle, which comes with Batik.
downloads: https://xml.apache.org/batik/svgviewer.html

 


Download

In the current version adaptations for the Affymetrix 500k GeneChip are implemented. The installers include the application and sample data:



Older versions:
Genomizer 1.1.0 Windows Installer
Genomizer 1.0.0 Windows Installer
Genomizer 1.0.0 Linux binaries
Genomizer 1.0.0 Linux source code
Genomizer 1.0.0 binaries for Redhat Fedora (Core 2)
Genomizer 1.0.0 source code for Redhat Fedora (Core 2)

Source code:
Genomizer Source
Converter Source
Batchrunner Source, Windows
Batchrunner Source, Linux

The following file contains a 500k SNP chip test data set for Genomizer. Please find more instructions in the 500k_Readme.txt which comes with the archive:
500k data set (242 MB)

Help:
Genomizer Tutorial (pdf)

Database schema:
JPG file
XML file

Database and schemas have been created with DBDesigner 4 from fabFORCE.net.

500k add-ons for Genomizer:
GenomizerHits (12 MB)
This tool extracts significant SNPs from the Genomizer output files according to user-defined thresholds. If required, adjacent SNPs can be added to the output.

 


Screenshots

Click to enlarge: