================================================================================
MOSAIK 2.2        Release Distribution Documentation                  2013-09-20
Wan-Ping Lee & Michael Stromberg    Marth Lab, Boston College Biology Department
================================================================================

News:

1. 2014-03-26 
   A bug causing incorrect bases of reverse complement alignments has been fixed.
   Please check any version greater than 2.2.19 for the fix.

2. Version 2.2 is about four-fold faster than previous by improving the Smith-
Waterman (SW) strategy and using SIMD SW [1]. This is also the version that we 
use on 1000 Genomes Project [2] Phase-III datasets.


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.


License:

MOSAIK is open source software, licensed under the GPL 2.0+, and is provided 
free-of-charge to all users. All we ask in return is that you acknowledge its 
use in publications, talks, etc.


Citation:

http://dx.plos.org/10.1371/journal.pone.0090581
We ask that you cite this paper if you use MOSAIK in work that leads to 
publication.


Obtaining:

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

    % git clone https://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 (2.2.3) then use:

        % git checkout 915f6feca4d321a79c29de34f6512f92b751b457



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".

If static libraries are not installed, please modify includes/linux.inc,
deleting "-static".



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.


References:
[1]: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
[2]: http://www.1000genomes.org/