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Mosaik 1.0.1388 Distribution Documentation
Michael Stromberg, Marth Lab                                          2010-02-01
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Compiling the source code
=========================

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

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 data directory and type Build, 
Align, and Assemble to run the appropriate scripts.

example:

> cd data
> ./Build.sh
> ./Align.sh
> ./Assemble.sh

The resulting ace file (c.elegans_chr2_test_II.ace) will be found in the
data/C.elegans_Chromosome2_Illumina/assembly/ directory, which can then
be viewed by utilities such as consed.

MOSAIK API
==========

C++ and perl code for parsing MOSAIK alignment archives can be found in the
MosaikTools directory.
