PathogenID is a bioinformatics pipeline that takes in raw sequencing data from Illumina machines and aligns the data to the Mycobacterium Tuberculosis reference genome. The alignment is the analyzed for variants and the variants are fed out to the GUI. Various graphs to visualize the data are generated and saved into subdirectories as well.
in the PathogenID directory
go build
./PathogenID
Select
Next
then
Run Pipeline
in the PathogenID directory the is a subdiretory called SampleData. Here you will find 2 fastq files you can run your pipeline on.
Resulting analysis files can be found in .../PathogenID/Analyses
after running an analysis, you can visualize your data by clicking on
Next
The analysis menu will generate plots in .../PathogenID/resources/ in subdirectories: Fastq_Plots, SamPlots, VCFPlots
In the go/src folder download go get gonum.org/v1/plot/... go get -u github.com/murlokswarm/mac
hg mercurial must be installed as well. You can determine this by typing
which hg
if hg turns up, and the two packages are in the go src along side this package and you're good to go!
-
Brendan Wee - Bweestyle
-
Jinke Liu
-
Xiaodi Pan
-
Chaoying Wang
See also the list of contributors who participated in this project.
This project is licensed under the MIT License - see the LICENSE.md file for details