Usefulaf is an all-in-one Docker/Singularity image for single-cell processing with Alevin-fry(paper). It includes the all tools you need to turn your FASTQ files into a count matrix and then load it into your favorite analysis environment. Specifically, this image includes:
simpleaf: A simplified interface to indexing and quantifying withalevin-fry.pyroe: An alevin-fry utility python package for building splici references, converting alevin-fry output formats, loading count matrix in Python, adding gene names (instead of just gene IDs) to output matrices, etc.fishpond::loadFry(): A R function for loading count matrix as SingleCellExperiment object.
For processing data simply using the usefulaf image, check our latest tutorial here.
For pulling the Singularity image, please run the following code in bash. Note that the image is
# if you use Docker
$ docker pull combinelab/usefulaf:latest
# if you use Singularity
$ singularity pull docker://combinelab/usefulaf:latest
Alevin-fry is a fast, accurate, and memory-frugal tool for preprocessing single-cell and single-nucleus RNA-seq data. You can read more about alevin-fry in alevin-fry pre-print, and paper.
This repository was created initially with scripts, functions, and utilities that are useful for preparing data for processing with alevin-fry, as well as for reading alevin-fry data into other packages for downstream analysis. It also accompanies a Docker/Singularity container containing all of this relevant software in one place. However, as alevin-fry has continued to grow, all of that relevant functionality found its way into other, more stable and permanent homes (e.g. pyroe for splici reference construction and loading data in Python, roe for splici reference constr5uction in R and fishpond for loading data in R). Finally, this repository also contained a bash script called simpleaf to simplify common workflows with alevin-fry. That, too, has evolved into its own (much more feature-rich and comprehensive) tool, living in its own repository (simpleaf).
As such, all the scripts and functions in this repository have been retired. However, as usefulaf is still the only place that provides all these functionalities, we decided to turn [usefulaf] as an all-in-one Docker/Singularity image that makes use of all those new tools listed above. That has replaced the older usefulaf image that made use of the varied assortment of scripts and tools hosted in this repository.