GitHub - lparsons/msg: Multiplexed Shotgun Genotyping

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
R.methodsS3		R.methodsS3
R.oo		R.oo
cmdline		cmdline
example		example
instructions		instructions
tests		tests
.gitignore		.gitignore
README		README
Utils.pm		Utils.pm
breakpoint-widths.R		breakpoint-widths.R
countalleles.c		countalleles.c
ded.R		ded.R
extract-ref-alleles.py		extract-ref-alleles.py
fastq_2_fasta.pl		fastq_2_fasta.pl
filter-sam.py		filter-sam.py
fit-hmm.R		fit-hmm.R
hmmlib.R		hmmlib.R
hmmprobs.c		hmmprobs.c
make-pileups.sh		make-pileups.sh
makefile		makefile
mapping_functions.py		mapping_functions.py
msg.pl		msg.pl
msgCluster.pl		msgCluster.pl
msglib.py		msglib.py
parent1or2-hmm.sh		parent1or2-hmm.sh
parse_BCdata2BWA.pl		parse_BCdata2BWA.pl
parse_and_map.py		parse_and_map.py
plot_error.R		plot_error.R
reformatFasta4sam.pl		reformatFasta4sam.pl
summaryPlots.R		summaryPlots.R
summary_mismatch.pl		summary_mismatch.pl
test_dependencies.sh		test_dependencies.sh
test_dependencies_R.R		test_dependencies_R.R
test_dependencies_R.sh		test_dependencies_R.sh
test_dependencies_executable.sh		test_dependencies_executable.sh
test_dependencies_python.py		test_dependencies_python.py
updateRef.pl		updateRef.pl
validate.py		validate.py
write-hmm-data.R		write-hmm-data.R

Repository files navigation

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)