SnpHub

SnpHub provides an interactive framework for exploration and visualization of large-scale genomic variation data to support analysis across diverse species.

Key Features:

• Implementation platform: Built on Shiny/R with a pre-building stage that consumes Variant Call Format (VCF) files and genome annotation files.
• Variant types supported: Supports querying and analysis of Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (INDELs) with associated annotation information.
• Query granularity: Enables access to variants and annotations by locus or gene and within user-defined sample sets.
• Visualization suite: Provides heatmaps, phylogenetic trees, haplotype networks, and geographical maps for visualization of genomic variation.
• Sample-specific sequences: Generates sample-specific sequences with SNPs and INDELs integrated into the reference sequence context.

Scientific Applications:

• Cross-species genomic variation analysis: Facilitates analysis of large-scale variant datasets across diverse species.
• Wheat and progenitor genomics: Implemented for wheat and its progenitors to support agricultural genomics investigations.
• Evolutionary and crop-improvement studies: Enables variant querying and visualization applicable to evolutionary analyses and crop improvement efforts.

Methodology:

A pre-building stage integrates Variant Call Format (VCF) files and genome annotation files into a local Shiny/R server environment for retrieval and visualization of genomic variation data.