Genome-Wdie Association Studies (GWAS) is an effective method for identifying disease susceptible genes. Pairing effective research methods with an in-depth understanding of genetic variation and the relation to traits of interest gives researchers a powerful platform for analysis.
Our SNP & Variation Suite™ (SVS) software delivers a world-class analytic tool and powerful visualizations in a user-friendly interface. No more struggling to coerce command-line software -- designed exclusively for human genetics. SVS supports a wide variety of analysis methods enabling you to quickly and easily identify variants related to disease susceptible genes and lead you beyond single marker associations.
User-Friendly Design
Our software tools manage, analyze, visualize and filter data all through a friendly user interface. We take great care in researching and implementing best practices as well as the latest methods and algorithms and serve them up in an intuitive way. We eliminate the need to learn how to script, unless you want to. While SVS provides a flexible, user-friendly interface on the front-end, it also provides full programmatic access on the back-end. So whether you're one who shudders at the thought of writing another line of code, or one who lives for it, SVS empowers you to do more than you ever thought possible.
SVS supports the broadest array of data formats for both import and export, eliminating the hassles of working with large data. You'll also find a host of tools that make it easy to format and recode data, merge data sets, create subsets, and more.
Support for a Wide Variety of Species and Genomes
No more coercing software designed for human genetics to work with the plant or animal species you're studying. SVS supports a wide variety of species, including different genomic builds for some. If your particular species is not included by default, you can easily add it along with corresponding annotations from a point-and-click interface. And switching between species and genomes is easy too. Just select the species you're studying from the project options tab or from a drop down menu in the genome browser and you're ready to go. See the full list of animal and plant genomes available in Golden Helix® software here.
Coverage Statistics
VarSeq provides coverage metrics in two forms. First, each variant displays data about the region in which it resides. This binding allows variants from suspect regions to be flagged or filtered out, which can help to prevent false positives. Second, each region in the BED file can be examined. This mode of analysis ensures that all the targeted regions were sequenced, which is crucial to preventing false negatives.
Clinical grade variant annotations
Included in VarSeq is functionality similar to SnpEff or Variant Effect Predictor. Each variant is mapped to all overlapping transcripts and information about the region where it is located (exon, intron, intergenic, etc.), sequence ontology (frame shift, synonymous, etc.), and HGVS notation (g dot, c dot, and p dot) is provided. You can chose to filter against the highest-impact annotation for each variant or the entire set of variant-transcript interactions.
Genome-Wide Association Studies (GWAS)
GWAS is growing rapidly in agricultural applications as a very effective method to identify genes of interest such as those affecting production and resistance traits. SVS provides you with a number of intuitive workflows from basic to advanced SNP analyses to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions. See the full description of our GWAS capabilities here.
Genomic Prediction
Whether you are using candidate genes or whole genomes, microarrays or next-generation sequencing, SVS delivers unparalleled performance on any size data. You can seamlessly navigate spreadsheets with billions of data points and easily plot variant maps, heat maps and genomic annotations across the entire genome for thousands of samples.
SVS provides the most complete set of statistical and visual analytic tools to help you quickly identify genetic variants or haplotypes and their association with traits of interest. We support SNP, CNV, or sequence data allowing you to perform a wide range of analyses. Not to mention all the time you'll save by not having to move large, complex datasets between multiple packages.
Powerful Visualizations
All visualizations in SVS are dynamic, interactive and integrative so you can quickly identify hot spots and navigate to areas of interest. Compare variant maps, LD structure or copy number patterns among breeds. Produce Manhattan plots for any number of dependent variables. Assess identity by descent or population stratification to locate problematic samples. The best part: any genomic-based plot can be visualized in an interactive genome browser alongside relevant annotations with proper genomic coordinates for the species you're studying.
Speed and Flexibility
Genomic Prediction is quickly becoming one of the most used tools for researchers interested in milk production, weight gain, and marbling or increased yield. SVS allows researchers to determine which animals or plants to continue breeding for desired traits including various means of defining the relationship between samples, the ability to validate models and visualize the results. See our full Genomic Prediction capabilities here.
Comprehensive Quality Assurance
High quality data is critical to high quality results. To ensure your data is of the highest quality, SVS provides the most comprehensive set of quality assurance tools helping you to not only assess the quality of your data, but remedy any problems as well.
Recommended Learning Materials
We have a variety of supplemental learning materials that are an excellent resource for anyone interested in the industry or our software solutions. Here are some of our recommended materials for you to check out related to VarSeq!
eBooks
Check out our free eBooks on a variety of different topics:
Webcasts
Watch an informative webcast featuring VarSeq in action!
Genomic Analyses for Palatability of Beef