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HATSEQ: Hypergeometric Analysis of Tiling-arrays and SEQuence data
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HATSEQ is a stand-alone application that is freely available for academic usage at http://www.erasmusmc.nl/hematologie/. 
HATSEQ is build on the proven methodology of HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data, http://www.biomedcentral.com/1471-2105/11/275
HATSEQ is is implemented in Matlab Mathworks and requires a x86-64 system and 4GB of free memory is highly recommended. 
HATSEQ is tested on Unix, Mac-OS and MS-Windows operating system. The runtime for a single experiment depends on the data size and can be decreased by enabling multi-threaded computations. It takes on average, with default parameter settings, 290 seconds (@1.87GHz) for the analysis of one sample. The installation of MATLAB or the MATLAB Compiler Runtime (MCR) is mandatory, e.g. MCR is a standalone set of shared libraries that enable full functioning of HATSEQ. The MCR installer is freely available at http://www.erasmusmc.nl/hematologie/. 

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MATLAB Compiler Runtime
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* A prerequister is the installation of MATLAB or the MATLAB Compiler Runtime (free). 
* Enable the installation of the MCR-installler and the configuration file. 
* Us the default settings of the installation

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Installation of PERL (required for CIRCOS)
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* Check the installation of "ActivePerl-5.14.2.1402-MSWin32-x64-295342"
* Perl modules are third-party code that adds functionality to the core language.
* Your installation of Perl will include core modules.
* In addition to these, you'll need to install the following modules to run Circos.
* http://circos.ca/tutorials/lessons/configuration/perl_and_modules/
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* The following packages are obligatory and need to be installed using the "Perl package manager":
  Config::General (v2.50 or later)
  GD
  GD::Polyline
  List::MoreUtils
  Math::Bezier
  Math::Round
  Math::VecStat
  Params::Validate
  Readonly
  Regexp::Common
  Set::IntSpan (v1.16 or later)
  Text::Format
* Some other packages that may be required:
  Data-Dumper
  File-Basename
  Getopt-Long
  IO-File
  List-Util
  Math-BigFloat
  Memoize
  Pod-Usage
  Time-HiRes

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Institutions
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Delft Bioinformatics Lab (DBL), Delft University of Technology, Delft, 2628 CD, The Netherlands
Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, The Netherlands
Netherlands Bioinformatics Centre (NBIC), The Netherlands 

