miCloud: a plug and play, on-premises bioinformatics cloud, providing seamless integration with Illumina genome sequencers

Benchtop genome sequencers such as the Illumina MiSeq or MiniSeq are revolutionizing genomics research for smaller, independent laboratories, by enabling access to low-cost Next Generation Sequencing (NGS) technology in-house. However, post-sequencing bioinformatics data analysis still presents a significant bottleneck. We developed miCloud, a bioinformatics platform for NGS data analysis, as a solution to fill the gap between the low-cost, widely available computational resources and lack of user-friendly bioinformatics software. The miCloud is highly modular and is based on Docker virtual machine containers for its components. There are three pipelines ready to execute with the miCloud upon installation, two for single and paired-end ChIP-Seq data, in addition to one more for paired-end RNA-Seq data. Additionally, we have integrated the Visual Omics Explorer (VOE) with the miCloud, to provide users with access to rich, interactive visualizations and publication-ready graphics from the pipeline outputs. Laboratories lacking NGS data analysis expertise can easily deploy miCloud in order to process data generated from in-house sequencing instruments, on a computer with 6-10 GigaBytes (GB) of memory and 1 TeraByte (TB) or less of storage.