Golden Helix
Accelerating the Quest for Significance
Whats New in SNP Variation Suite 7.4
With over 30 new features, the fourth installment of SNP & Variation Suite 7 empowers you to explore your data as never before. Identify rare causal variants with a new Sequence Analysis Module. Improve your GWAS and CNV results with state-of-the-art workflows. Dramatically increase your productivity. And gain greater insights with the most advanced genome browser. This is just a taste of what you'll discover on your way to more impactful research. Enjoy!
- Introducing the first integrated solution for DNA Next-Gen Sequencing analysis
- Large Data.
- Unparalleled Performance.
- Streamlined Data Import
- Variant Filtering
- Rare Variant Analysis
- New state-of-the-art GWAS and CNV quality assurance methods
- Identity by Descent and Inbreeding Coefficient
- LD Pruning
- Autosome Heterozygosity
- Gender Misidentification
- Quartile Summary Statistics
- Multidimensional Outlier Detection
- Derivative Log Ratio Spread
- Chromosomal Aberration Screening 
- Wave Detection
- Correction Percentile-Based Winsorizing
- Significantly faster, and improved copy number analysis workflows
- GPU Accelerated Copy Number Segmentation
- Streamlined Import of Affymetrix CEL Files
- Support for Affymetrix 2.7M Cytogenetics Array 
- Improved CNAM Output Analysis
- More powerful genome browsing and annotation track management
- Custom Annotation Tracks (WGA)
- New Network Annotation Tracks (WGA)
- Set Default Genome and Annotation Tracks (WGA)
- On-demand, advanced feature development with improved python
- Productivity enhancers
SNP, CNV, & Family Analysis • GWAS
Genetic research scientists who work with massive amounts of complex data generated by very sophisticated, very expensive devices, are typically handicapped when it comes to interpreting or getting maximal value out of their data. Though there is no shortage of the rough, specific-purpose software routines that precipitate out of academic research projects, these programs lack the very features their users need to accelerate research and make breakthroughs: an intuitive, high-performance interface that enables researchers to use the software effectively; robust analysis and visualization tools that help them make and understand findings; comprehensive technical support for when they have challenges; and cross-platform compatibility that facilitates work with collaborators and disparate tools. Without a product with these qualities, researchers are forced to spend an inordinate amount of time and money building expertise in computer science instead of their research.
SNP & Variation Suite
Golden Helix' SNP & Variation Suite (SVS) is a unique set of software tools created specifically for genetic research. SVS helps researchers easily analyze, visualize, and publish important discoveries on genetic, phenotypic, and clinical data, getting them past the frustration of having to use incompatible, difficult programs instead of focusing on their research, making important findings, and publishing their results.
SVS includes modules for SNP and copy number analyses on both population and family-based cohorts, including very sensitive algorithms for finding copy number breakpoints on individual samples in clinical cytogenetics. Further, SVS is compatible with all major genotyping and sequencing platforms and is used by hundreds of genetic and pharmacogenetic researchers in the industry, government, and academia the world over. With hundreds of citations in peer reviewed articles, SVS enjoys a reputation for performance, usability, reliability, and fast time to results.
ANALYTIC SOLUTIONS
SNP Analysis
Get the most out of your SNP data with the most complete set of genotype analysis tools.
Copy Number Variation Analysis
From cytogenetics to GWAS, SVS 7 delivers the most powerful CNV analysis tools.
LD and Haplotype Analysis
Powerful new plotting and analytics capabilities for linkage disequilibrium and haplotypes.
Genome-Wide Association
Take GWAS to a new level with unparalleled performance on large-scale data.
Runs of Homozygosity Analysis
Identify patterns of extended homozygosity and then run statistical tests for association.
Family-Based Analysis
Cutting-edge analytics for virtually any family study design and ascertainment condition.
Data Management
Easily manage data of any size and type on a conventional desktop computer.
Data Editing and Enrichment
Real-time data editing, manipulation, and enrichment on large-scale data.
Quality Assurance
A robust toolset for quickly assessing and remedying sample and marker issues.
Interactive Visualization
Explore data and results with unprecedented whole genome navigation and visualization.
Scripting and Integration
Innovate, integrate, and automate with a fully-programmatic Python scripting interface.
SVS MODULES
HelixTree
HelixTree is the core module of the SNP & Variation Suite. Its unique set of conventional and leading edge analytic tools empower you to quickly and easily perform a broad array of workflows for genetic association studies.
CNAM
CNAM, in conjunction with other SVS 7 modules, offers a complete set of tools for processing raw intensity data, identifying regions of copy number variation (CNV), visualizing copy number data, and performing association analysis on a variety of copy number covariates.
PBAT
Developed in collaboration with Dr. Christophe Lange of Harvard's School of Public Health, Golden Helix PBAT delivers an exclusive and extensive array of advanced statistical routines for the design and analysis of family-based SNP and CNV association studies.
Whole Genome Analysis Module
The Whole Genome Analysis Module incorporates several technologies and methods designed to overcome the statistical and computational challenges of large-scale whole genome analysis.
Regression Module
Perform advanced linear and logistic regression, stepwise regression, and permutation tests with numeric variables and recoded genotypes.
SVS Viewer
SVS Viewer makes collaboration easy, and it's completely free. Load projects or individual datasets created by someone with SVS 7. Then you can manipulate spreadsheets, edit node annotations, augment existing plots, or create entirely new ones.
TECHNICAL REQUIREMENTS
SVS will run well on just about any conventional laptop, desktop, or server. However, there are several considerations in choosing new hardware that will give you the optimal experience while mitigating budget impact.
Standard (Moderate power adequate for most Single Named User and Lab Licenses)
- Single dual-core processor (Quad-core processors are getting cheaper, becoming an attractive option)
- 32-bit Windows 7, XP, Vista, Linux, or Mac OS X 10.5
- 2-4GB of RAM
Advanced (For Universal Server Licenses, systems used for CNV segmentation, or for large projects)
- Two quad-core processors (eight cores)
- 64-bit Windows 7, XP, Vista, Linux, or Mac OS X 10.5
- (If for a server license: Windows Server 2003 64-bit, Windows Server 2008 64-bit, or 64-bit Linux)
- 8-16GB+ of RAM
About Golden Helix
Founded in 1998 in Bozeman, Montana by Dr. Christophe Lambert, Golden Helix is a leading bioinformatics company that enables the world's leading researchers to find or diagnose the genetic causes of disease, drug safety, and drug efficacy - advancing the promises of personalized medicine. Using Golden Helix' genetic analysis software and analytic services, these researchers are able to make sense of complex, expensive genetic data, turning it into novel, actionable findings. Further, leveraging core competencies in genetic analysis and predictive analytics, Golden Helix develops complex genetic diagnostic and cytogenetic solutions that enable the diagnosis or prediction of disease. Golden Helix' clients include several of the top ten pharmaceutical companies (including GalxoSmithKline, Johnson & Johnson, and Roche), numerous biotechs, and over 100 academic and government research organizations around the world.
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