Genomic tools in the cloud: the new frontier in omics data analysis
Creators: name: Barcelona-Cabeza, Rosa
name: Tomás, David
name: Paytuvi, Andreu
name: Melis, Guadalupe Gómez
name: Cigliano, Riccardo Aiese
name: Sanseverino, Walter
Publisher: name: F1000 Research Limited
Year: 2019

description: The knowledge and understanding acquired from genomics research can be applied in very diverse fields, including medicine, biotechnology and agriculture. Current sequencing platforms (Next Generation Sequencers - NGS) generate big data that need to be sorted, curated, integrated, analyzed and interpreted. Due to the size and complexity of such data, most geneticists or biologists fail to process their own data or it becomes time consuming. In addition, due to the diversity of genomic applications, informaticians usually do not have all the knowledge required to fully understand the biological "problem" of the researcher, making it impossible to reach a practical solution. Therefore, it is crucial to find a solution to efficiently manage the large amount of data produced as well as to find a solution to analyze and interpret genomic data in an easy and efficient way.<br><br>Genomic variants obtained by sequencing already influence clinical decisions. They influence how physicians perform patients diagnose, prognostic evaluations and therapeutic choices. However, very few pipelines are versatile enough to call all types of genomic variations as they require very different algorithms, increasing the computational cost and highlight the need of a single platform, integrated and trustworthy.<br><br>On the basis of the above, we are developing an user-friendly platform that allow, in an accessible and scientifically robust way, to analyze and interpret genomics variations without need of informatic knowledge. For the time being, we have developed different pipelines for the analysis and identification of different types of variations (SNP, INDEL and CNV) as well as a parents-child trios analysis pipeline. Results are obtained in about 2,5 hours for 100x WES analysis (8 threads) and in 10 hours for 15x WGS analysis (8 threads). Interpretation and visualization of results is one of the bottleneck in these workflows, therefore, we have also built a visualization platform, which allows to display and browse dynamically in the results of SNPs/INDELs calls, and a database for data storage, which allow the user to have all samples stored in a unique environment without space problems. The visualization interface has two sections: variant browser and panels. Variant browser section focuses on the patient, allowing to visualize all the variants of a sample, whereas the panels section focuses on diseases, allowing to check whether a patient has known pathogenic variants related to any disease. <br><br>Our platform could introduce a disruptive innovation allowing researchers to perform analysis and integration of omic data easily, quickly and affordably. It is focused on professionals who wants to use genomics to perform decision making gathering genomics data with other evidences. For example, hospital professional who want upload their data and directly perform result interpretation, without giving rise to intermediate step as data analysis and processing. They could check directly the presence or absence of variations related to any disease of interest, enabling a quick decision-making approach. This is an innovative solution that aims to cover the gap between production and data analysis, specifically in the field of NGS data. The final result would be the democratization of significant part of the NGS bioinformatics.