A web-server framework to explore and visualize large genomic variation data in lab and its applications to wheat and its progenitors

Decreased sequencing costs now allow a laboratory to investigate genomic varia-tions in hundreds or thousands of samples by resequencing or genotype-by-sequencing (GBS). Managing and exploring the large genomic variation data require programming skills. The public genotype querying databases for many species may not be frequently updated and are still lim-ited in samples. Many individual samples have unique genomic variations in either cancer or crop studies. Here we present SnpHub, a Shiny/R-based server framework for retrieving, analyzing and visualizing the large genomic variation data within a lab. After the pre-building process based on the provided VCF files and genome annotations, the local server allows users to instantly access the SNP/INDELs and annotation information by locus or gene, and for user-defined sam-ple sets, without any programming background. The users can also easily analysis and visualize the genomics variations in heatmap, phylogenetic tree, haplotype-network, or geographically, and get genomic sequences replaced by sample-specific SNPs and INDELs. SnpHub can be applied to any species, and here we provide demo-servers for wheat progenitors using the public GBS data. SnpHub and its tutorial are available as http://guoweilong.github.io/SnpHub/.