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

Abstract 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 limited 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/.