FASTGenomics – a platform to share single-cell RNA sequencing data and analyses using reproducible workflows 

Recent technological advances enable genomics of individual cells, the building blocks of all living organisms. Single cell data characteristics differ from those of bulk data, which led to a plethora of new analytical strategies. However, solutions are only useful for experts and currently, there are no widely accepted gold standards for single cell data analysis. To meet the requirements of analytical flexibility, reproducibility, ease of use and data security, researchers at Comma Soft, Bonn, in collaboration with the Schultze lab at LIMES Institute in Bonn, developed  FASTGenomics  (  as a powerful, efficient, versatile, robust, safe and intuitive analytical ecosystem for single-cell transcriptomics .

FASTGenomics is designed as a platform for single cell RNA-seq data open to the scientific community. A major feature is to provide highest reproducibility and transparency for single cell data analysis to the whole community. The platform provides publicly available datasets and apps for calculation and visualization. Analyses are accompanied by a detailed summary (see Figures below).


Due to its open structure, it is easy to contribute to FASTGenomics – just visit the  github page. The code is fed into the FASTGenomics runtime by means of docker containers. You can imagine docker containers as a self-sustaining, portable workplaces which have certain benefits: Using docker containers provides full reproducibility and helps avoiding “works only on my machine” problems. Moreover, using docker containers allows you to use any programming language and framework you prefer while keeping things as simple as possible for us to integrate your app into an analysis.

Availability –  FASTGenomics is available at:

Scholz et al. (2018) FASTGenomics: An analytical ecosystem for single-cell RNA sequencing data. BioRXiv, 272476. [article]

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