================================================================================
MOSAIK 2.0        Release Distribution Documentation                  2013-04-01
Wan-Ping Lee & Michael Stromberg    Marth Lab, Boston College Biology Department
================================================================================

Overview

MOSAIK is a stable, sensitive and open-source program for mapping second and 
third-generation sequencing reads to a reference genome. Uniquely among current 
mapping tools, MOSAIK can align reads generated by all the major sequencing 
technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, 
Ion Torrent and Pacific BioSciences SMRT.



Obtaining:

To download MOSAIK, please use git to download the most recent development tree.

    % git clone git://github.com/wanpinglee/MOSAIK.git


Or, download it from google code webpage:
    
    https://code.google.com/p/mosaik-aligner/downloads/list


If you encounter issues with the development HEAD, or simply wish to obtain the
most recent stable revision (2.1.78) then use:

        % git checkout 5dfdc8e723f031f2



Compilation:

MOSAIK requires g++ and the standard C and C++ development libraries.
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 E.Coli.

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 (read.mka.bam) will be found in the
demo/fastq directory.
