Phytozome Population Diversity Visualization in JBrowse: A very large Dataset Case Study

Phytozome (http://phytozome.jgi.doe.gov/) is a plant comparative genomics web portal offering access to genome annotations and gene family data. Our current release includes 49 species from a diverse set of land plant and Chlorophyte taxa. We continue to enrich our reference genome annotations with NGS data sets and corresponding analyses of gene expression (across tissue types, developmental stages, and environmental conditions) and genetic diversity (across natural and designed populations). However, the scale of these datasets is increasing rapidly, posing unique challenges for visualization systems like JBrowse that perform graphical rendering within end-user web browser client software. In addition, despite JBrowse support for tabix indexing and data file compression, the metadata associated with large population sample sizes can result in larger files that tax the limits of typical end user hardware (memory and processor). One illustrative example is a population of 544 Populus trichocarpa trees, where Illumina reads were aligned to the reference assembly and analyzed by GATK to call single nucleotide and indel variation. Work to build an efficient display of this data in JBrowse while minimizing client-side data access and rendering resource consumption is discussed.