GenomeQuest

Category Cross-Omics>Sequence Analysis/Tools and Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract GenomeQuest is one of the world’s leading sequence data management (SDM) platforms. 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.

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.

Advanced Workflows and Analysis -- GenomeQuest allows researchers to focus on science instead of IT details. From a single dashboard, research teams have access to world-class resources - discovery tools, compute resources, public datasets - to perform all upstream and downstream analysis including whole- and multi-genome analysis.

Key Capabilities -

1) Store, manage, and compare sequences and annotations;

2) Assemble and align sequences from any instrument;

3) Interactively query and analyze results;

4) Merge and re-analyze with findings from colleagues and public studies;

5) Data/result sharing with colleagues through dashboards;

6) Data export to other discovery tools, including desktop visualization;

7) Integration with other tools and services via an ‘all-level’ API; and

8) Genome center performance from the database engine and data center architecture.

Commonly used pre-built workflows include:

1) RNA-Seq - RNA-Seq stands to replace existing transcript profiling technologies as it measures all RNA in a sample, Not just the RNA that can be probed for using traditional chips. GenomeQuest provides an advanced workflow that integrates best-of-breed open source technologies in a commercially supported environment to measure gene expression and to discover novel splice variants.

2) Whole Genome Analysis - The GenomeQuest Whole Genome Analysis suite finds and annotates genomic variation.

3) ChIP-Seq - GenomeQuest ChIP-Seq solution provides state-of-the-art tools across the entire workflow, including for alignment, peak modeling, and interactive analysis. Integrating the popular Model based Analysis for Chip-Seq “MACS” peak modeling software, it allows for over 15 key parameters to be set and multiple runs to be stacked and analyzed collectively.

4) Metagenomics - GenomeQuest’s Metagenomics workflow allows you to compare millions of sequences against all of the world’s reference data to determine the composition of the DNA in the sample.

This workflow has been used in infectious disease applications, diagnostics, air quality, soil change over time, defense applications, and indeed, to rescue the California Syrah grape from decline symptoms due to a previously unknown virus.

5) Patent Research - Search, Mine, and Monitor the World’s Patent Sequence Data - Overall, more and more law firms, pharmaceutical firms, biotech companies, and academia are using GenomeQuest as an integrated solution for all their IP sequence searching needs: including IP validity, freedom-to-operate, patent infringement, and business opportunity.

6) Multi-Genome Analysis - GenomeQuest’s Multi-Genome Analysis highlights the underlying power of the GenomeQuest Engine by allowing you to compare the genomes of arbitrarily large populations. The workflow’s inputs are genomes that have already been analyzed using GenomeQuest’s Whole Genome Analysis process.

7) Molecular Diagnostics - High-throughput sequencing represents a compelling cost-reduction for molecular diagnostics where large numbers of genes need to be sequenced. Through the manufacturer's Whole Genome Analysis annotation capability, GenomeQuest has the ability to perform molecular diagnostics in silico.

Note: All GenomeQuest capabilities are available as a hosted web service running on the GenomeQuest data center or deployed on an organization’s compute infrastructure behind their firewall. All functionality and data are available to researchers from their desktop or mobile web browser.

GenomeQuest Workflows -- All GenomeQuest Workflows are delivered in an easy-to-use, integrated environment. They package all bioinformatics details - including read and reference data, scientific algorithms, all third party integration, all parameters, and the compute environment - into a simple form-based interface.

Researchers query and analyze results using an interactive sequence browser. All data, parameters, and results can be shared with colleagues and teams using the GenomeQuest collaborative environment.

GenomeQuest workflows are built to scale to thousands of samples, each with billions of reads. They support all popular sequencing machines (including Illumina, SOLiD, 454, and PacBio) and all common formats (including FASTQ, FASTA, SAM/BAM, VCF, SVA, and others).

High Performance Infrastructure -- The GQ-Engine is purpose-built to store, analyze, and manage sequence and annotation billions of reads and thousands of samples.

As organizations grow into NGS, GenomeQuest’s distributed architecture maintains performance and accuracy across all critical dimensions: users, data, and tools. Also, because the compute environment, the data storage, and the management of data and workflows are all central, shared resources, the entire discovery environment of the research organization can also scale comfortably to NGS.

Note: GenomeQuest’s hosting architecture presently has capacity for processing 150 genomes per month, and will soon be scaling to thousands of genomes per month.

World’s Largest Collection of Annotation -- GenomeQuest integrates one of the world’s largest collections of annotation and reference databases for IP clearance, variation discovery, and genome-wide annotation of variation.

Core sequence databases include:

GenBank sequences from NIH; RefSeq sequences from NCBI;

ENSEMBL mRNA; IgBlast nucleotide database; ProbeDB from NCBI;

Protein Data Bank - nucleotide sequences; DrugBank Pro nucleotide sequences;

GENESQ sequences in patents from Thomson-Reuters; and SIPO Chinese patent sequences.

In addition, extensive genome variation annotation exists and is available for resequencing studies. These include:

dbSNP; RefSeq genes; RefSeq exons; RefSeq proteins; OMIM;

Repeats; Splice sites; pharmGKB; and GeneTests.

Sequences and annotations are systematically collected, cleaned, and normalized. All data is accessible for integrated searching and comparisons from the dashboard, workflows, or the APIs. Data is updated, recalculated, and refreshed as new data and studies are released.

Users and organizations can also add, combine, and save their own datasets in GenomeQuest - removing all silos from their sequence and annotation data across their projects.

Built-In Collaboration -- GenomeQuest makes it easy for research teams to securely collaborate on small and large projects across groups, companies, and research partnerships.

As a browser-based application, GenomeQuest allows researchers to perform work and connect however and whenever they want. With No software to install, researches can focus on making discoveries instead of spending time worrying about patches, upgrades or downloads.

Designed specifically for collaborative and distributed environments, GenomeQuest enables the secure sharing of workflows, custom integrations, and analysis tools in addition to public and private datasets.

Unified Database for all Sequence Data -- Sequences, variations, and annotations from all sources can be unified into a single, continuous database that is accessible to all researchers. Sources include project and company data, partnership studies, and public reference datasets - removing all silos.

Researchers can perform analysis - including the generation of comprehensive variation reports - on any selection from the unified database. Bioinformatic teams can build more advanced applications through common, programmatic access to the entire collection of data.

Open Platform for Powerful Applications -- GenomeQuest serves as an open platform that allows bioinformatics teams to spend more time on science applications and less time on IT details. A complete application programming interface (API) provides full access to a full range of bioinformatics services, including:

1) Engine-level operations for comparisons and querying;

2) Workflow-level processes for capturing science/business logic; and

3) Administration, sharing, and compute resources.

Bioinformatics teams and researchers can use the API to:

1) Customize GenomeQuest and/or built-in workflows;

2) Build new workflows and scientific applications;

3) Integrate other discovery tools into GenomeQuest;

4) Integrate or cloud-enable existing algorithms/pipelines;

5) Access GenomeQuest reference databases;

6) Scale services to next-generation sequencing (NGS) volumes;

7) Securely publish workflows and applications to extended communities; and

8) Consolidate support across users, instruments, and tools.

The open platform interoperates with popular RDBMS’s. Using a best-of-breed approach, GenomeQuest utilizes the RDBMS to manage relational data - including admin, metadata, and user annotations - while itself efficiently and comprehensively managing sequence data and reference annotations.

System Requirements

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Manufacturer

Manufacturer Web Site GenomeQuest

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G6G Abstract Number 20131R

G6G Manufacturer Number 101120