Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
SVA is a JAVA program, designed to run on a 64-bit LINUX platform with a 64-bit JAVA environment installed. SVA was designed to be a LINUX desktop software tool.
Standard Full Edition
The minimum hardware requirement for SVA standard edition is a 64-bit LINUX workstation equipped with at least 32GB of RAM and 120GB of free hard disk. This workstation also needs to support a Graphical User Interface (GUI) environment, for example, using the X Window System.
However, we would like to recommend a 64-bit LINUX workstation equipped with 48GB of RAM or more, and 1TB of free hard disk or more.
The developers are using the machine specified below to run SVA and found it productive. Please note we do not intend to recommend the specific model or manufacturer, but rather list the specifications here for your reference.
Please note this lite evaluation edition does not provide the full annotation functions, but can be only used to load the example dataset for testing purposes.
A 64-bit Sun JAVA environment with version no earlier than 1.6.0_17 is required to run SVA. For details of JAVA releases, visit Sun JAVA website.
If you desire to access SVA through a Windows PC to a LINUX workstation or server, a PC X server then is necessary. Multiple such products are available, for example, X-Win32 .
For Mac users, X server may be available from the operating system. You may try "ssh -x [your LINUX server]" to establish such connection. Or you may need additional software tool, like X11.
© 2011 Dongliang Ge, PhD.