PEGG: Prime Editing Guide Generator¶
Click here to read the Nature Biotechnology article¶
PEGG is a python package that designs prime editing guide RNAs (pegRNAs) and base editing guide RNAs (gRNAs) for use in precision genome editing. Unlike the existing, web-based programs for pegRNA design, PEGG is suitable for designing thousands of pegRNAs at once, giving users the ability to design entire libraries of pegRNAs and gRNAs. Uniquely, PEGG can design paired pegRNA or gRNA-sensor cassettes that include a synthetic version of the target locus, allowing for the calibration of guide editing activity in pooled screens (see above bioRxiv preprint for more information).
PEGG’s main functions are:
Generating pegRNAs or gRNAs based on a list of input mutations. The input format is extremely flexible, allowing for users to input a list of genome coordinates or sequences with desired edits.
Ranking and filtering these pegRNAs based on their properties, including On-Target (Azimuth) Scores.
Automated oligo generation (with the option to include a synthetic “sensor” region).
Automated pegRNA/gRNA library design with included safe-targeting mutations, non-targeting guides, and silent substitution controls.
Visualization Tools for pegRNA and gRNA design.
PEGG has recently been updated to version 2.0, with new features including (1) increased input mutation format flexibility, (2) Dynamically computed Azimuth on-target scores, (3) a new base editing module, (4) improved library design functionality, as well as some minor bug fixes with INS/DEL design.
Installation¶
PEGG is available through the python package index. To install, use pip:
pip install pegg
Note¶
PEGG has been tested with python versions 3.9 and 3.10. Python versions higher than 3.10 are not compatible with the scikit-learn package version needed to compute protospacer on-target scores. To get it to install, you may need to use a virtual environment :
conda create -n myenv python=3.9
Additionally, some users (particularly on Windows) have reported installation issues stemming from the cyvcf2 package used for translating ClinVar IDs to a format compatiable with PEGG. A version without this package and its functionality is available for local pip installation in the following dropbox link (pegg-2.0.92-py3-none-any.whl) .
Contents:
PEGG is an open source python package. If you use PEGG, please cite it using the following citation:
Gould, S.I., Wuest, A.N., Dong, K. et al. High-throughput evaluation of genetic variants with prime editing sensor libraries. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02172-9