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R.methodsS3
R.oo
cloud
cmdline
dependencies
example
example_MSG_toy
instructions
tests
tools
.gitignore
README
TQSfastq.py
Utils.pm
barcode_splitter.py
breakpoint-widths.R
combine.py
countalleles.c
create_stats.py
ded.R
extract-ref-alleles.py
fastq_2_fasta.pl
filter-sam.py
fit-hmm.R
grepfqparser.py
hmmlib.R
hmmprob_to_est.py
hmmprobs.c
make-pileups.sh
makefile
mapping_functions.py
msg.pl
msgCluster.pl
msgUpdateParentals.pl
msglib.py
parent1or2-hmm.sh
parse_BCdata2BWA.pl
parse_and_map.py
plot_error.R
print_dependencies.sh
reformatFasta4sam.pl
send_email.py
summaryPlots.R
summary_mismatch.pl
test_dependencies.sh
test_dependencies_R.R
test_dependencies_R.sh
test_dependencies_executable.sh
test_dependencies_perl.pl
test_dependencies_python.py
updateRef.pl
validate.py
version
write-hmm-data.R

README

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

NOTE: Most of these packages can be found in the dependencies directory for you to 
extract and install as needed on your system.

Python (2.6.4)
numpy (recent versions should be fine)
bwa (0.5.7)
samtools (0.1.9-3)  ! Newer versions of Samtools will not work !
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)
Perl Modules (IO::Uncompress::Gunzip)
    -- A command like this should work on Unix Desktop Systems:
    -- perl -MCPAN -e 'install IO::Uncompress::Gunzip'
mailer (Python package: http://pypi.python.org/pypi/mailer) - optional; for sending email alert when run completes

### 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)

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