VeraCode Assay Designer software

The VeraCode Assay Designer software streamlines the development of low- to mid-plex genotyping assays using VeraCode Universal Capture Beads. Simply import list of desired targets in FASTA format by dbSNP accession number, or directly insert sequence information and select the design parameters. The software outputs multiple allele-specific primer extension assay designs scored on multiplex compatibility, GC content, melting temperature, likelihood of primer dimmers, and folding. Results are easily exported for straightforward purchasing of consumables and running on the BeadXpress Reader.

VeraCode Assay Designer Highlights
Streamlined Interface: Simply input target sequences and the software automatically designs multiplex assays
Flexible Assay Design: Automatically incorporate capture bead sequence or manually assign bead codes
Customizable Design Parameters: Manually select parameters for increased control, use pre-set criteria, or allow the software to use preset design parameters.

Software Link:  VeraCode Assay Designer software
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SNP & Variation Suite - Genomic software

SNP & Variation Suite is the most powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale, complex genomic data. It's fast, easy-to-use, and runs on conventional desktop computers enabling you to interact with your data as never before. Both statistically and visually, you can explore the relationships among vast amounts of clinical patient data, environmental factors, and genetic variants to understand the cause of disease and other traits - without writing a single line of code (unless you want to).
Details
YOUR DATA. YOUR ANALYSIS. YOUR DISCOVERY.

SNP & Variation Suite is the most powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale, complex genomic data. It's fast, easy-to-use, and runs on conventional desktop computers enabling you to interact with your data as never before. Both statistically and visually, you can explore the relationships among vast amounts of clinical patient data, environmental factors, and genetic variants to understand the cause of disease and other traits - without writing a single line of code (unless you want to).

ANALYTIC SOLUTIONS

SNP Analysis
Get the most out of your microarray data with the most complete set of SNP analysis tools.

Genome-Wide Association
Take GWAS to a new level with unparalleled performance on large-scale data.

Next-Generation Sequencing Analysis
Latest tertiary analysis methods for DNA
next-generation sequencing.

Copy Number Analysis
Optimal results with a complete set of quality assurance, CNV detection, and analysis tools.

LD and Haplotype Analysis
Powerful new plotting and analytics for linkage disequilibrium and haplotypes.

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.

Genome Browser and 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.

Runs of Homozygosity Analysis
Identify patterns of extended homozygosity and run statistical tests for association.

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.

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.

Sequence Analysis Module
Rare variants require new methods that don't work in traditional common variant studies. With the introduction of an entirely new Sequence Analysis Module you now have access to the latest tertiary analysis methods to help you make the most sense of all that next-gen sequencing data.

PBAT
Developed in collaboration with Dr. Christoph 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.

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.



Software Link: SNP & Variation Suite

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GenomeQuest - Sequence data management (SDM) platform

At the core of GenomeQuest is the GQ-Engine - a database engine that is purpose-built for storing, managing, and analyzing sequence data at NGS scale.

GenomeQuest is the world's leading sequence data management (SDM) platform. Researchers use state-of-the-art tools to store, manage, and analyze genomic data. Bioinformatics teams get a development platform to customize workflows, build applications, and unify their sequence data environment. IT and business managers can efficiently scale to NGS across discovery operations.

Science Applications
GenomeQuest provides cutting-edge computational, querying, and visualization tools along with applications that accelerate research and discovery.

Built-In Collaboration
A web-based dashboard offers easy access to everything your team needs - including compute resources, sequence datasets, and discovery tools.

High Performance Infrastructure
GenomeQuest is purpose-built for large-scale sequence data management and analysis, utilizing cloud-based, embarassingly parallel" computing.

Unified Database for all Sequence Data

Sequences

Software Link: GenomeQuest
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Sequencher 5.0 - DNA sequence data anaylsing Software

Sequencher 5.0 from Gene Codes Corporation takes you from DNA sequence data to results easier and faster than ever! Over 20 years of daily use by biologists in labs around the world have refined Sequencher's tools and interface. You get the power and speed to get accurate results from your DNA analysis, and get back in the lab more quickly. Whether you need DNA sequence assembly and analysis tools for next-generation or traditional (Sanger or Capillary Electrophoresis) DNA data sets, Sequencher 5.0 will guide you toward results.

Next-generation DNA data sets:
  • Maq and GSNAP alignment algorithms
  • SNP analysis and methylation studies
  • Tablet Viewer

Traditional DNA data sets:
  • Multiple, configurable DNA Assembly algorithms
  • Comprehensive DNA sequence editing tools
  • Full support of sequence data confidence values

Next-generation or Traditional DNA data analysis features:
  • Powerful reference sequence alignment
  • Variance Table to discover SNPs quickly and easily
  • Extensive data import and export capabilities
  • NCBI BLAST search
  • Forensic mtDNA profiling

Software Link:  Sequencher 5.0

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DNAnexus - Sequence Data analysing software


DNAnexus provides solutions for both DNA sequencing centers growing their next-gen capacity, and researchers working with next-gen sequence data. Our web-based platform solves the data management and analysis challenges common to both with a single, unified system.

DNAnexus is built from the ground up to run on Amazon Web Services, the world's leading cloud computing provider. Our solution delivers not just software, but also all the computing and storage infrastructure. 100,000s of CPUs and 100s of petabytes of storage are available to you through DNAnexus, which acquires those resources on demand, allowing our pricing to mirror your usage. We support sequencing operations and research organizations of virtually any size, with absolutely no upfront hardware investment needed.

For core facilities with one instrument or sequence centers with 100 instruments, you can connect your sequencing output to DNAnexus in as little as 10 minutes. Learn more about what DNAnexus can do for your next-gen data management.

For researchers with a single lane of data, or for large commercial life science research organizations, DNAnexus can give you the right tools for your work, and the ability to scale up your research instantly in the future. Get started immediately without any setup or configuration.

Software Link: DNAnexus - Sequence Data analysis




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CLC Main Workbench

CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.
Details
A comprehensive workbench for advanced DNA, RNA, and protein analyses

CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

CLC Main Workbench is available on Windows, Mac OS X, and Linux platforms.
Detailed Pricing
Static single computer license: $1999 for industrial customers, $399 for academic customers
Network licenses: $3999 for industrial customers, $799 for academic customers

Software Link: CLC Main Workbench
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CLC Science Server

CLC Science Server is an advanced Next Generation Sequencing focused three- tier solution offering secure, powerful, and flexible bioinformatics computing on a server located centrally in your organization.

Details
An advanced & powerful three-tier solution

CLC Science Server is an advanced Next Generation Sequencing focused three- tier solution offering secure, powerful, and flexible bioinformatics computing on a server located centrally in your organization.

The three main components are:

CLC bio offers installation, customization, and integration
Server software running on all major platforms (Windows, Mac OS X, and Linux)
Database backend: Either your existing database(s) or CLC Bioinformatics Database (Microsoft SQL Server 2003 & 2008, Oracle, mySQL, PostgreSQL, or H2)
Client software: Any CLC Workbench, any Web browser, and any custom developed clients can access the server concurrently

Among others, CLC Science Server provides you:
A powerful and modern three-tier server architecture
Flexible options of executing centralized services
Easy integration with other applications and services
Powerful database communication and data integration
Secure access control framework and central action logging

Software Link: CLC Science Server
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