MSG: Multiplexed Shotgun Genotyping
http://genomics.princeton.edu/AndolfattoLab/MSG.html
https://github.com/JaneliaSciComp/msg
http://www.ncbi.nlm.nih.gov/pubmed/21233398

### Dependencies ###
  Run test_dependencies.sh to check for the existence of dependencies
Python (2.6.4)
bwa (0.5.7)
samtools (0.1.9-3)
biopython-1.53
Pyrex-0.9.9
pysam-0.1.2 (apply fix as described here: http://code.google.com/p/pysam/issues/detail?id=22&can=1&q=dandavison0)
R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3)

### Installation instructions ###
git clone git://github.com/JaneliaSciComp/msg.git
cd msg
make

### Toy Example ###
The toy example is useful to check that MSG and dependencies are installed and functioning correctly.
TODO

### Example with Real Data ###
Download the data from NCBI's Sequence Read Archive and MSG config and barcodes file
 - example/get_sample_data.sh (requires wget)