Microservices to connect genetic maps to (pan)genomes (KB-38-001-015)

Functional annotation of plant genomes is often based on data generated from genetic experiments such as QTL and GWAS analyses. Markers from cross-specific genetic maps are positioned on reference genomes to delineate regions and genes of interest. High resolution genetic maps and pangenomes or multiple reference genomes per species are now becoming available with NGS technologies. The next step will be the annotation of genetic information into those references.

Current bottleneck are genetic map generation, extraction of publicly available genetic maps from literature and mapping against reference genomes, which is still far from an automatic process. In this project, we will analyse different sets of data where key genetic maps have been generated, and integrate with our microservices project to show the genetic distance and QTL information for fair-ifying the data and preparing for plant functional pangenomics.

 

We will use the microservices platform currently developed in the Microbrewery platform as a starting point. This platform allows for the analysis of over 70 yeast strains using graph databases, Apache Spark and Cytoscape / Circos / Reactome for visualizations. The tool is connected to several online databases for direct access to that knowledge.