Absolutely RADic(a)l methods for analyzing single-cell sequencing data (written in Rust)!

alevin-fry is a suite of tools for processing single-cell sequencing data. It consumes RAD files generated by 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).

Alevin-fry is available for both x86 linux and OSX platforms using bioconda.

With bioconda in the appropriate place in your channel list, you should simply be able to install via:

$ conda install alevin-fry

If you want to use features or fixes that may only be available in the latest develop branch (or want to build for a different architecture), then you have to build from source. Luckily, cargo makes that easy; see below.

Alevin-fry is built and tested with the latest (major & minor version) stable Rust (currently 1.45). Building should be as easy as:

$ cargo build --release

subsequent commands below will assume that the executable is in your path. Temporarily, this can be done (in bash-like shells) using:

$ export PATH=`pwd`/target/release/:$PATH

Alevin-fry is under active development. However, you can find the documentation on read the docs. We try to keep the documentation up to date with the latest developments in the software.