This package helps you desing oligos for riborid protocol for rRNA depletion. The package requires input rRNA sequence or genbank file from your target organism. If no sequence information is available for your organism/strain, you can try using sequence from closely related organism as rRNA sequences tend to be highly conserved.
Since RiboRid Design is currently under development, the recommended method to
install riborid_design is to use the editable pip installation. It is
recommended to do this inside a virtual environment or in a conda
environment. This is because we require
Python 3.8 for certain functionalities.
To create the conda environment:
conda create -n riborid python=3.8 conda activate riborid
Next, download the github repository:
git clone https://github.com/SBRG/RiboRid_Design.git
Then install with pip using the -e flag:
python -m pip install -e .
This method of installation will automatically update your package each time you pull from this repository.
To update your code, run the following from your local riborid folder:
git pull
Lastly, use conda to install muscle
!! The latest version of muscle (v5.1) is not compatible. Use muscle (v3.8) instead
Muscle v3.8 is available through etetoolkit repository (last confirmed 11/11/2022):
conda install -c etetoolkit muscle
To run riborid in default mode, all you need is the genbank file of your target organism. With the genbank file, simply run the following from command line:
design_oligos 'path/to/genbank/file' --ftype 'genbank'
The data will be stored in the newly created rrd_res folder. The rrd_primers.fa contains all the primer sequences while the rrd_oligosdf.csv contains the metadata associated with each of the sequences.