Overview
Alevin-fry is a suite of tools designed for rapid, accurate, and memory-frugal processing of single-cell and single-nucleus sequencing data. It consumes RAD files generated by piscem or salmon alevin, performing operations like generating permit lists and estimating the number of distinct molecules from each gene within each cell. The tool prioritizes safety, accuracy, and efficiency in terms of both time and memory. It is designed as a successor to alevin, subsuming its core features while introducing new capabilities and significantly improving performance. Alevin-fry supports enhanced transcriptomes using tools like pyroe, allowing for spliced and intronic or spliced and unspliced analysis. Output can be easily integrated into the R ecosystem using the fishpond package and assessed using alevinqc.