Metadata-Version: 2.4
Name: magestic
Version: 2.0.0
Summary: Multiplexed CRISPR library design and analysis for functional genomics
Project-URL: Homepage, https://github.com/kevinroy-lab/magestic
Project-URL: Repository, https://github.com/kevinroy-lab/magestic
Project-URL: Bug Tracker, https://github.com/kevinroy-lab/magestic/issues
Author-email: "Kevin R. Roy" <kevinrjroy@gmail.com>
License: MIT
Keywords: CRISPR,MAGESTIC,barcode,donor-DNA,functional-genomics,guide-RNA,yeast
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Description-Content-Type: text/markdown

# MAGESTIC

**M**ultiplexed **A**ccurate **G**enome **E**diting with **S**hort, **T**rackable, **I**ntegrated **C**ellular barcodes

Tools and pipelines for CRISPR-based genome editing in yeast.

## Contents

### Guide-Donor Oligo Design

Scripts for designing MAGESTIC guide-donor oligonucleotides:

- `generate_guide_donor_oligos_for_natural_variants_from_vcf.py` - Design oligos for natural variants from VCF
- `generate_amino_acid_variant_guide_donor_oligos_for_saturation_editing.py` - Design oligos for saturation mutagenesis
- `guide_donor_oligo_functions.py` - Shared functions for oligo design

### Data Processing

- `process_batch_editing_data.py` - Process batch editing experiments
- `process_overlapping_reads.sh` - Handle overlapping paired-end reads
- `collapse_identical_merged_reads_min_counts.py` - Collapse duplicate reads

### Genome Utilities

- `GTF_GFF_manipulation.py` - GFF/GTF file parsing and manipulation
- `bedgraph_computation.py` - Generate bedgraph coverage files

### Variant Effect Prediction (VEP)

The VEP pipeline for running variant effect prediction models is maintained in a **separate private repository**.

**Access:** Contact Kevin Roy (kevinroy@stanford.edu) for access to the VEP-pipeline repository.

**Supported models:**
- Evo2 7B/40B - DNA sequence log-probability scores
- Yorzoi - RNA expression predictions from DNA
- Shorkie - RNA expression (8-fold ensemble)
- ESM1-v - Protein variant effect scores

## Requirements

- Python 3.8+
- Biopython
- pandas, numpy
- samtools (for FASTA indexing)

## Citation

If you use MAGESTIC, please cite:

> Roy KR, et al. (2018). Multiplexed precision genome editing with trackable genomic barcodes in yeast. *Nature Biotechnology* 36:512-520.

## License

MIT License - see individual files for details.
