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R.methodsS3
R.oo
cmdline
example
instructions
tests
.gitignore
README
Utils.pm
breakpoint-widths.R
countalleles.c
ded.R
extract-ref-alleles.py
fastq_2_fasta.pl
filter-sam.py
fit-hmm.R
hmmlib.R
hmmprobs.c
make-pileups.sh
makefile
mapping_functions.py
msg.pl
msgCluster.pl
msglib.py
parent1or2-hmm.sh
parse_BCdata2BWA.pl
parse_and_map.py
plot_error.R
reformatFasta4sam.pl
summaryPlots.R
summary_mismatch.pl
test_dependencies.sh
test_dependencies_R.R
test_dependencies_R.sh
test_dependencies_executable.sh
test_dependencies_python.py
updateRef.pl
validate.py
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
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)