SVDetect is distributed under GNU Public License (GPL). All its source codes and data are freely available to both academic and commercial users.

The latest version can be downloaded at the SourceForge download page.

Requirements

Perl 5.8.x, or newer, is recommended.

In addition of the core modules that come with your Perl distribution,

running SVDetect need to install additional modules:

Config::General

Tie::IxHash

Parallel::ForkManager

You can find the required perl modules "Tie::IxHash" and "Parallel::ForkManager" in the lib/ directory or from CPAN (www.cpan.org).

To install the Config::General module, you can use CPAN (if CPAN module is installed)

> perl -MCPAN -e shell

% install Config::General

or use the search.cpan.org website to find directly the module.

Optional components

Circos software installation for graphical visualization, available at the following address:

http://mkweb.bcgsc.ca/circos

SAMtools for working on compressed bam files, available at: http://samtools.sourceforge.net

BEDtools is required to compare SVs between multiple datasets, available at: http://code.google.com/p/bedtools

UCSC Genome Browser: http://genome.ucsc.edu

Sample datasets

The SVDetect package contains one example of datasets to illustrate the common usage of the program

(Neuroblastoma and normal cell lines, 50bp Illumina mate-pair reads).

All data files for generating mate-pair mapping clusters are already included in the test_sample/ directory.

Additional data files are required to get copy-number profiles and are available at the following address:

http://sourceforge.net/projects/svdetect/files/Data/Neuroblastoma_supp_data.tar.gz/download

Uncompress the archive file and copy the content into the test_sample/Neuroblastoma directory.