Mason

Manuel Holtgrewe

Abstract

We present a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes. The C++ source code is extensible, and freely available under the GPL/LGPL.

Installing

Currently, the only way to install mason, is from source. Assuming you have Subversion, CMake make and a compiler installed under Linux/Mac Os X:

svn co http://svn.seqan.de/seqan/trunk seqan-trunk
mkdir -p seqan-trunk-build/release
cd seqan-trunk-build/release
cmake ../../seqan-trunk
make mason
./bin/mason --help

On Windows, perform a Subversion checkout of the URL http://svn.seqan.de/seqan/trunk, e.g. to a directory called seqan-trunk. Then, open a command line window, go to this directory and generate a Visual Studio file using CMake:

mkdir ...\seqan-trunk-build\vs10
cd ...\seqan-trunk-build\vs10
cmake ...\seqan-trunk -G "Visual Studio 10"

This will generate a Visual Studio file in the subdirectory “apps” which you can use to compile the program mason. Alternatively, you can follow the instructions of the article “Getting Started” in the SeqAn trac.

More Information

Is available in the README file in core/apps/mason.

References

Last Update 21. August 2013