czbiohub-sf / protoSpaceJAM

CRISPR knock-in design at scale

protoSpaceJAM

💻 protoSpaceJAM is a python package to design guide RNA and repair donors for CRISPR knock-in experiments
🌐 protoSpaceJAM can also be accessed through our web portal at http://protospacejam.czbiohub.org/
📖 Detailed information about protoSpaceJAM can be found in our preprint

 

Key features:

• Fully standalone, no calling to other bioinformatics servers
• Sophisticated guide RNA ranking system (details)
  • Specificity weight
  • Penalize cuts near exon-intron junctions etc.
  • Penalize cuts far away from the payload insertion site
• Sophisticated DNA donor design (details)
  • Recode to prevent recut
  • Recode to facilitate payload insertion and prevent recut
  • Automated selection of of ssDNA donor for maximum chance of payload insertion and prevent recut
  • Scan and trim hard-to-synthesis motifs
  • Center the DNA donor around the region containing the payload and recoded bases.
  • Enforce maximum length of DNA donor
• Use/generate pre-computed genome-wide guide RNAs and their properties for fast runtime

 

Installation

Clone the repository

git clone https://github.com/czbiohub/protoSpaceJAM

Go the repository directory, switch the branch if running branch other than master

cd protoSpaceJAM
git checkout main

Create conda environment and activate it

conda create -y -n protospacejam python=3.9 && conda activate protospacejam

Install protoSpaceJAM

pip install .

Download and unzip pre-computed data

💾 41G disk space (82G temporary) required for (human🕺, mouse🐭 and zebrafish🐟 genomes) x (SpCas9, VQR-SpCas9 and enAsCas12a)

python ./protoSpaceJAM/util/download_precomputed_results.py

If the download process is disrupted, rerun the same command to resume.
If prompted to download with browser, place the file in protoSpaceJAM/protoSpaceJAM/ and rerun the command with an additional argument --use_local

[less disk space option]
💾 25G disk space (50G temporary), add additional argument --SpCas9_only

👉 If you like to precompute your own gRNAs, please follow here

Run a quick test to verify installation

python ./protoSpaceJAM/tests/run_quick_test_pJAM.py

A successful test will have a printout similar to Ran 2 tests in 14.644s OK at the end.

full test suite can be run with

python ./protoSpaceJAM/tests/run_full_test_pJAM.py

A successful test will have a printout similar to Ran 2 tests in 1873.836s` at the end.

 

Usage

conda activate protospacejam
protoSpaceJAM --path2csv input/test_input.csv --outdir output/test

 

License

Distributed under the terms of the BSD-3 license, "protoSpaceJAM" is free and open source software