simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry

Abstract

AbstractSummaryThealevin-fryecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as thealevin-fryecosystem itself expands and grows, it is becoming increasingly important to manage the complexity ofalevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introducesimpleaf, a program that simplifies the processing of single-cell data using tools from thealevin-fryecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.Availability and implementationSimpleafis written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repositoryhttps://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation forsimpleafis available athttps://simpleaf.readthedocs.io/en/latest/and tutorials forsimpleafare being developed that can be accessed athttps://combine-lab.github.io/alevin-fry-tutorials.