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alevin-fry website  

alevin-fry is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data. It consumes RAD files generated by salmon alevin, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell. The focus in alevin-fry is on safety, accuracy and efficiency (in terms of both time and memory usage).

Environment Modules

Run module spider alevin-fry to find out what environment modules are available for this application.

System Variables

  • HPC_ALEVIN-FRY_DIR - installation directory


If you publish research that uses alevin-fry you have to cite it as follows:

He, D., Zakeri, M., Sarkar, H. et al. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022).