Python program for universal design of targeted-enrichment probes from multiple input datatypes. Can be used to generate probe sets for ultraconserved elements, anchored enrichment, RAD-capture, etc.
Citation: Chafin TK, Douglas MR, Douglas ME. 2018. MrBait: Universal identification and design of targeted-enrichment capture probes. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty548
Documentation: https://mrbait.readthedocs.io/
Conda package: https://anaconda.org/tylerkchafin/mrbait
I currently support native installation on Linux and Mac OS. MrBait is not natively supported on Windows, however will run using the Linux subsystem for Windows 10 (see: https://docs.microsoft.com/en-us/windows/wsl/install-win10). MrBait was tested using the Ubuntu Windows-10 subsystem.
Regardless of OS, the easiest way to install is using the conda package manager (https://conda.io/docs/):
conda install mrbait -c tylerkchafin -c bioconda -c conda-forge
If you are concerned about conflicting dependencies, you can also create a contained virtual conda environment for mrbait and associated dependencies:
#conda call to create a blank python3.6 environment named "mrbait"
conda create -n mrbait python=3.6
#activate the mrbait conda environment.
source activate mrbait
#add some channels
conda config --env --add channels bioconda --add channels conda-forge
#install mrbait
conda install -c tylerkchafin mrbait
#run mrbait:
mrbait -v example.VCF <etc>
...
...
#exit environment
source deactivate
#note that you can now reactivate your mrbait environment at any time by typing:
source activate mrbait
#and then exit again just as before
source deactivate
You can update to the latest conda release by typing:
conda update -c conda-forge -c bioconda -c tylerkchafin mrbait