sortscore: Sort-seq MAVE scoring and visualization using Python

A growing number of tools enable the analysis of large variant libraries produced by multiplexed assays of variant effects (MAVEs). Experiments using fluorescent reporters and fluorescence-activated cell sorting sequencing (FACS-seq or Sort-seq) can coarsely quantify a given variant's impact on phenotypes such as transcription activity. Existing bioinformatics tools for Sort-seq data broadly fall into two categories: methods that model a genotype-phenotype landscape to infer latent variant phenotypes, and methods that directly estimate individual variant scores from experimental binned counts. Within this second category, sortscore provides an activity score computed directly from observed counts without fitting a model, retaining the original experimental scale when bin median values are known.We present sortscore, a python package that incorporates a standard Sort-seq scoring method and normalization across sorted samples, technical replicates from separate sort times, and across oligos in tiled experiments. It also provides convenient heatmap visualizations. This software was used to analyze DMS experiments for the transcription factor GLI2. This work seeks to lower the barrier to entry and provide a clear starting point for scoring Sort-seq cell-based functional assays. This extends the availability of well-documented and reproducible data analysis protocols to a wider community employing MAVE techniques.

The package can be downloaded from PyPI using the pip installer. The code is also freely accessible and available for reuse through a Public GitHub repository (MIT License). Installation instructions, documentation, and tutorials are accessible at the sortscore GitHub repository: https://github.com/dbaldridge-lab/sortscore. A snapshot of the code and data is available on Zenodo: https://doi.org/10.5281/zenodo.22119031.

Supplementary figures are available at Bioinformatics online.