
TechRxiv
A preprint server for health sciences.

An efficient and flexible tool for processing single-cell sequencing data, focused on single-cell transcriptomics and feature barcoding.

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.
Alevin-fry is a suite of tools designed for rapid, accurate, and memory-frugal processing of single-cell and single-nucleus sequencing data.
Explore all tools that specialize in transcriptome alignment. This domain focus ensures alevin-fry delivers optimized results for this specific requirement.
Processes Reduced Alignment Data (RAD) files generated by piscem or salmon for efficient quantification.
Generates permit lists to identify valid cell barcodes for downstream analysis.
Estimates the number of distinct molecules from each gene within each cell.
Generates output compatible with the fishpond R package for downstream analysis.
Supports enhanced transcriptomes (spliced + intronic or spliced + unspliced) using pyroe.
Provides a dedicated wrapper/workflow runner in the simpleaf repository for streamlined processing of data.
Install Rust using rustup.
Clone the alevin-fry repository from GitHub.
Build the tool from source using `cargo build --release`.
Add the executable to your PATH using `export PATH=`pwd`/target/release/:$PATH`.
Install piscem or salmon for RAD file generation.
Consult the ReadTheDocs documentation for detailed usage instructions.
Utilize the simpleaf wrapper for streamlined workflows.
Familiarize yourself with the input RAD file format.
Use bioconda for installation, if applicable.
All Set
Ready to go
Verified feedback from other users.
"Alevin-fry is highly regarded for its speed, accuracy, and memory efficiency in single-cell RNA-seq data processing."
Post questions, share tips, and help other users.

A preprint server for health sciences.

Connect your AI agents to the web with real-time search, extraction, and web crawling through a single, secure API.

A large conversational telephone speech corpus for speech recognition and speaker identification research.

STRING is a database of known and predicted protein-protein interactions.

A free and open-source software package for the analysis of brain imaging data sequences.

Complete statistical software for data science with powerful statistics, visualization, data manipulation, and automated reporting in one intuitive platform.