Getting Started¶
mrbait has been tested on Mac and Linux operating systems and is primarily supported on those platforms. However, Windows users can easily install using the built-in Linux subsystem for Windows 10.
In-development code can be found on the Github page: https://github.com/tkchafin/mrbait
If you find any issues with the program, please email me at tkchafin@uark.edu or submit as an issue on Github, which can also be used for submitting feature requests. When submitting bugs or issues, please include input files, your command-line call, and any output MrBait produced to the screen or output files.
Availability¶
Functioning releases can be found at: https://github.com/tkchafin/mrbait/releases
Source code: https://github.com/tkchafin/mrbait
conda package: https://anaconda.org/tylerkchafin/mrbait
Dependencies¶
mrbait is written for Python3, and requires Python version >= 3.6.0. The recommended method of acquiring Python and all other dependencies is via the Anaconda distribution, as outlined in Section 3.3. A full list of dependencies is given below.
mrbait can optionally use the following programs during bait development:
For these utilities, please cite the following: Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics. 1-:410. Doi:10.1186/1471-2105-10.421
Rognes R, Flouri T, Nichols B, Quince C, Mahe F. 2016. VSEARCH: A versatile and open source tool for metagenomics. PeerJ. 4:e2584. Doi: 10.7717/peerj.2584
Installation¶
By far the easiest way to acquire and install mrbait is via conda, a command line interface for managing and installing packages. Download and install anaconda for Python 3.6 here: https://www.anaconda.com/download/. If you are wanting a minimal environment, or a faster install, you can also use the Miniconda distribution (https://conda.io/miniconda.html) with the same commands. After installation, be sure to test that conda is installed by typing conda info, which will print information about your installation. Note, you may first need to reload your bash environment by typing source ~/.bashrc or source ~/.bash_profile on Mac. Assuming success, the installation process is then very straightforward:
#This command tells conda that the code and dependencies for mrbait can
#be found in ‘channels’ bioconda, conda-forge, and tylerkchafin.
conda install mrbait -c tylerkchafin -c bioconda -c conda-forge
#If you would like to instead install the latest development version, you can
#clone the github repository and
#install MrBait like so (assuming you have git installed):
git clone https://github.com/tkchafin/mrbait.git
cd mrbait
python ./setup.py install
You will then need to manually install both vsearch and blast, only if you install directly from the GitHub source using the setup.py installation. These will be installed for you if you used conda.
Windows users: MrBait is installable using the built-in Linux subsystem for Windows 10. I have only tested using the Ubuntu OS subsystem configuration but assume that other Linux distros would work equally well. If you prefer, you can also use a Linux installation on a virtual machine, or installed portably on a USB-attached drive, although this may impact performance. Contact me at tkchafin@uark.edu if you have any issues getting mrbait installed, or feel free to launch an ‘Issue’ on the GitHub page.
HPC users: One of the reasons I recommend using conda to manage your Python environment, is that it keeps your packages separate from the system environment, which you often will not have permissions to modify. Anaconda will instead install your own local flavor of Python in your home directory, where is will also install any additional packages you choose to add.
BLAST and VSEARCH: conda will also install both BLAST and VSEARCH and place them within your conda environment. If you would like to manually manage versions of these programs, or use an existing installation, you can provide the paths to those binaries using the –vsearch and –blastn commands for mrbait.
Running mrbait¶
Assuming you have completed the recommended conda install, mrbait and it’s Dependencies should already be in your path and is now fully ready to go. You can verify successful installation, and view the help menu, by typing: mrbait -h
Instructions for bait design are provided as arguments (see Section 5 for thorough usage instructions, and Section 8 for tutorials). For example, to generate baits of length 80, tiled across target regions with an overlap of 40 bases, from a Multiple Alignment File (MAF) “example.maf”:
mrbait -M example.maf -b 80 -s tile=40
Or, to also filter for only alignments including 5 or more individuals, and of length >500:
mrbait -M example.maf -b 80 -s tile=40 -l 500 -c 5