SnpHub

SnpHub is a Shiny/R-based server framework for retrieving, analysing, and visualizing large-scale genomic variation data that can be easily set up on any Linux server. After a pre-building process based on the provided VCF files and genome annotation files, the local server allows users to interactively access single-nucleotide polymorphisms and small insertions/deletions with annotation information by locus or gene and to define sample sets through a web page. Users can freely analyse and visualize genomic variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence variations.