GitHub - elifesciences-publications/msg: Multiplexed Shotgun Genotyping

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Name		Name	Last commit message	Last commit date
Latest commit History 257 Commits
R.methodsS3		R.methodsS3
R.oo		R.oo
cloud		cloud
cmdline		cmdline
dependencies		dependencies
example		example
example_MSG_toy		example_MSG_toy
instructions		instructions
tests		tests
tools		tools
.gitignore		.gitignore
LICENSE		LICENSE
README		README
TQSfastq.py		TQSfastq.py
Utils.pm		Utils.pm
barcode_splitter.py		barcode_splitter.py
breakpoint-widths.R		breakpoint-widths.R
check_dependencies_R.R		check_dependencies_R.R
combine.py		combine.py
countalleles.c		countalleles.c
create_stats.py		create_stats.py
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
filter_hmmdata.pl		filter_hmmdata.pl
fit-hmm.R		fit-hmm.R
fitParentalHMM.sh		fitParentalHMM.sh
grepfqparser.py		grepfqparser.py
hmmlib.R		hmmlib.R
hmmprob_to_est.py		hmmprob_to_est.py
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
msgUpdateParentals.pl		msgUpdateParentals.pl
msglib.py		msglib.py
optimizeParameters.pl		optimizeParameters.pl
parent1or2-hmm.sh		parent1or2-hmm.sh
parse_BCdata2BWA.pl		parse_BCdata2BWA.pl
parse_and_map.py		parse_and_map.py
plotSegregation.R		plotSegregation.R
plot_error.R		plot_error.R
print_dependencies.sh		print_dependencies.sh
reformatFasta4sam.pl		reformatFasta4sam.pl
send_email.py		send_email.py
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_perl.pl		test_dependencies_perl.pl
test_dependencies_python.py		test_dependencies_python.py
updateRef.pl		updateRef.pl
validate.py		validate.py
version		version
write-hmm-data.R		write-hmm-data.R

Repository files navigation

### This code is associated with the paper from Binshuang et al., "A large genomic insertion containing a duplicated follistatin gene is linked to the pea aphid male wing dimorphism". eLife, 2020. http://dx.doi.org/10.7554/eLife.50608
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)