alevin-fry

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  "desc": "Efficient and flexible tool for processing single-cell sequencing data",
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  "github_readme_excerpt": "\u003cimg alt=\"logo\" src=\"https://github.com/COMBINE-lab/alevin-fry/raw/master/docs/logo.png\" width=\"200\"\u003e\n\n# alevin-fry ![Rust](https://github.com/COMBINE-lab/alevin-fry/workflows/Rust/badge.svg) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/platforms.svg)](https://anaconda.org/bioconda/alevin-fry) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/license.svg)](https://anaconda.org/bioconda/alevin-fry) ![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/combine-lab/alevin-fry?style=flat-square)\n\n`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`](https://github.com/COMBINE-lab/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).\n\nYou can read the paper describing alevin fry, \"Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data\" [here](https://www.nature.com/articles/s41592-022-01408-3), and the pre-print [on bioRxiv](https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1).\n\n**Note**: We recommend using [`piscem`](https://github.com/COMBINE-lab/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.\n\n### Getting started with `alevin-fry` and dedicated documentation\n\nWhile this `README` contains some useful information to get started and some pointers, `alevin-fry` has it\u0027s own [dedicated documentation site](https://alevin-fry.readthedocs.io/en/latest/), hosted on `ReadTheDocs`.\n\n### More information \n\n* [**Quickstart guide using the `simpleaf` wrapper**](https://combine-lab.github.io/alevin-fry-tutorials/20",
  "github_repo": "COMBINE-lab/alevin-fry",
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  "github_topics": [
    "10x",
    "quantification",
    "rna-seq",
    "rust",
    "single-cell",
    "single-cell-rna-seq",
    "transcriptomics"
  ],
  "homepage": "https://github.com/COMBINE-lab/alevin-fry",
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  "license": "BSD-3-Clause",
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  "ruby_source_path": "Formula/a/alevin-fry.rb",
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