Dependencies

Dependencies

GASiC was tested with the software listed below. Older versions of the listed software might still work, but are not tested.

• Python 2.6, http://www.python.org/

• NumPy 1.6.1, http://numpy.scipy.org/

• SciPy 0.10.0, http://www.scipy.org/
• BioPython 1.58, http://biopython.org/wiki/Biopython
• pysam 0.6, http://code.google.com/p/pysam/

In order to use the GASiC Quality Check (optional), you will need Matplotlib:

• Matplotlib 1.1.0, http://matplotlib.sourceforge.net/

GASiC calls alignment tools and read simulators from the command line. These tools must be installed and added to the PATH before they can be used with GASiC. We tested GASiC with the following tools:

• bowtie, http://bowtie-bio.sourceforge.net/index.shtml
• bowtie2, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

• bwa, http://bio-bwa.sourceforge.net/bwa.shtml

• Mason, http://www.seqan.de/projects/mason/

• dwgsim, http://dnaa.sourceforge.net/

We developed and tested GASiC on a Linux system. Windows or Mac users can either download our [Virtual Machine], where GASiC is preinstalled, or try make GASiC run on their system. There should be no reason why GASiC should not be portable to other systems, yet some fine tuning may be required.