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Latest commit 2a45785 Mar 8, 2016 @YourePrettyGood YourePrettyGood committed with gregpinero Added handling of haplodiploid species
MSG should now be able to handle haplodiploid species, since we can now
specify all scaffolds as being sex chromosomes (sexchroms=all).
Remember to specify the haploid sex as "male" in the barcodes file, and
the diploid sex as "female".

Signed-off-by: Greg Pinero <gregpinero@gmail.com>
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R.methodsS3
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example Added difffac parameter to msg.cfg file Jan 28, 2015
example_MSG_toy Update msg.cfg Sep 10, 2014
instructions
tests
tools
.gitignore
README several features: fix msg.chrlength, max_read_length, parameter for c… Oct 8, 2014
TQSfastq.py Changes for new mapping algorithms Mar 13, 2012
Utils.pm
barcode_splitter.py
breakpoint-widths.R First commit Apr 6, 2011
combine.py
countalleles.c
create_stats.py
ded.R
extract-ref-alleles.py
fastq_2_fasta.pl
filter-sam.py
fit-hmm.R Added handling of haplodiploid species Apr 8, 2016
grepfqparser.py
hmmlib.R
hmmprob_to_est.py Added another row to file format, added memory and time tracking Mar 4, 2014
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 more dependency printing Oct 15, 2013
reformatFasta4sam.pl
send_email.py
summaryPlots.R
summary_mismatch.pl
test_dependencies.sh
test_dependencies_R.R Added dependency checking, .gitignore Jun 6, 2011
test_dependencies_R.sh
test_dependencies_executable.sh
test_dependencies_perl.pl
test_dependencies_python.py
updateRef.pl first attempt at making trimming and updating updating parents steps … May 22, 2012
validate.py
version Update version Sep 22, 2015
write-hmm-data.R Fixing grep call Oct 3, 2014

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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