We are currently working on renewing the funding supporting the development of 
our sequencing analysis tools. If you find this software, or any of our other 
tools useful in your research, and are willing to provide a letter of support to 
this effect, would you please contact the PI, Gabor Marth via email at 
marth (at) bc (dot) edu? We will be very thankful for your feedback.



================================================================================
Mosaik 2.0        Release Distribution Documentation                  2011-04-25
Michael Stromberg & Wan-Ping Lee    Marth Lab, Boston College Biology Department
================================================================================

Compiling the source code
=========================

Just enter the src directory, glance at the README file, and type "make"



Running the demo
================

To see a full list of the available command line options, enter the bin
directory and run any of the program without any extra parameters.

Included in this release is an Illumina data set featuring reads C. elegans
chromosome 2.

To test Mosaik with this data set, just enter the demo directory and type Build, 
and Align to run the appropriate scripts.

example:

> cd demo
> ./Build.sh
> ./Align.sh

The resulting bam file (c_elegans_chr2_test.mka.bam) will be found in the
demo/sequence_archives directory.