A Single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework
Jonathan R Manning,
Maria A Doyle,
Posted 08 Jun 2020
bioRxiv DOI: 10.1101/2020.06.06.137570
Posted 08 Jun 2020
Background : The vast ecosystem of single-cell RNA-seq tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatic community leans once more towards the large computing requirements and the statistically-driven methods needed to process and understand these ever-growing datasets. Results : Here we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatic framework provides tools, workflows and trainings that not only enable users to perform one-click 10x preprocessing, but also empowers them to demultiplex raw sequencing data manually. The downstream analysis supports a wide range of high quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal and clustering. The teaching resources cover an assortment of different concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal. Conclusions : The reproducible and training-oriented Galaxy framework provides a sustainable HPC environment for users to run flexible analyses on both 10x and alternatively derived datasets. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy Community provide a means for users to learn, publish and teach scRNA-seq analysis. ### Competing Interest Statement The authors have declared no competing interest.
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