Sushi
Sushi is an agile and extensible data analysis framework that brings innovative concepts to Next Generation Sequencing bioinformatics. Sushi lets bioinformaticians wrap open source tools like e.g. bowtie, STAR or GATK into apps and provides natively a commandline and a web interface to run these apps. Users can script their analysis as well as do an analysis-by-clicking in their browser. When running an app Sushi takes care of all aspects of documentation: Input data, parameters, software tools and versions are stored persistently. Sushi accepts meta-information on samples and processing and lets the user define the meta-information he needs in a tabular format. Finally, all results, the associated logs, all parameters and all meta-information is stored in a single, self-contained directory that can be shared with collaborators. Altogether, Sushi as a framework truly supports collaborative, reproducible data analysis and research. At the Functional Genomics Center, Sushi is tightly integrated with B-Fabric and shares the authentication, sample information and the storage. The production version of Sushi is currently being further integrated in the overall B-Fabric framework.
Sushi has been presented at the ECCB 2014, Strasbourg. The presentation is available external pageherecall_made
A demo version is available here.