COMBINE-lab / alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
https://alevin-fry.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics
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alevin-fry Rust Anaconda-Server Badge Anaconda-Server Badge GitHub tag (latest SemVer)

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 piscem or 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).

You can read the paper describing alevin fry, "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data" here, and the pre-print on bioRxiv.

Note: We recommend using piscem as the back-end mapper, rather than salmon, as it is substantially more resource-frugal, faster, and is a larger focus of current and future development.

Getting started with alevin-fry and dedicated documentation

While this README contains some useful information to get started and some pointers, alevin-fry has it's own dedicated documentation site, hosted on ReadTheDocs.

More information

FAQs

Are you curious about processing details like whether to use a sparse or dense index? Do you have a question that isn't necessarily a bug report or feature request, and that isn't readily answered by the documentation or tutorials? Then please feel free to ask over in the Q&A.

Sister repositories

Installing from bioconda

Alevin-fry is available for both x86 linux and OSX platforms using bioconda. On Apple silicon, you can either build (easily) from source (see below) or run alevin-fry under the rosetta 2 emulation layer.

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

$ conda install -c bioconda alevin-fry

Installing from crates.io

Alevin-fry can also be installed from crates.io using cargo. This can be done with the following command:

$ cargo install alevin-fry

Building from source

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) stable version of Rust. While it will likely compile fine with slightly older versions of Rust, this is not a guarantee and is not a support priority. Unlike with C++, Rust has a frequent and stable release cadence, is designed to be installed and updated from user space, and is easy to keep up to date with rustup. Thanks to cargo, 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

Citing alevin-fry

If you use alevin-fry in your work, please cite:

He, D., Zakeri, M., Sarkar, H., Soneson, C., Srivastava, A., and Patro, R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022). https://doi.org/10.1038/s41592-022-01408-3

BibTeX:


@Article{He2022,
author={He, Dongze and Zakeri, Mohsen and Sarkar, Hirak and Soneson, Charlotte and Srivastava, Avi and Patro, Rob},
title={Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data},
journal={Nature Methods},
year={2022},
month={Mar},
day={01},
volume={19},
number={3},
pages={316-322},
issn={1548-7105},
doi={10.1038/s41592-022-01408-3},
url={https://doi.org/10.1038/s41592-022-01408-3}
}