Elysium: RNA-seq Alignment in the Cloud

Motivation RNA-sequencing (RNA-seq) is currently the leading technology for genome-wide transcript quantification. Mapping the raw reads to transcript and gene level counts can be achieved by a variety of aligners and pipelines. The diversity of processing options reduces interoperability. In addition, the alignment step requires significant computational resources and basic programming knowledge. Elysium enables users of all skill levels to perform a uniform and free RNA-seq alignment in the cloud. Results The Elysium infrastructure is comprised of four components: A file upload API that enables storage of FASTQ files on Amazon S3 without Amazon credentials; an API to handle the cloud alignment job scheduling for uploaded files; and a graphical user interface (GUI) to provide intuitive access to users that do not have command-line access skills. Availability The Elysium source code is available under the Apache Licence 2.0 on GitHub at: https://github.com/maayanlab/elysium The service of cloud based RNA-seq alignment is freely accessible through the Elysium GUI at: http://elysium.cloud