SMRT compatible analysis products
In continuing our efforts to deliver expanded genetic insight, we have selected a wide variety of experienced analytical partners.
In continuing our efforts to deliver expanded genetic insight, we have selected a wide variety of experienced analytical partners. These organizations support your research by offering services and solutions that complement SMRT Analysis products, providing a deeper understanding of your sequencing data. Our partners offer services and solutions in the following areas:
- Compute infrastructure
- LIMS
- Genome assembly, demultiplexing + mapping
- Variant detection
- Tertiary analysis
- Data analysis services
Compute infrastructure
Description
BioSoft Integrators’ High Performance Computing (HPC) on premise solutions are turnkey appliances that are Pre-Configured, Pre-Tested and Designed Specifically for the Application of NGS Analysis. Our HPCs are pre-loaded with all open-source analysis packages so when the system arrives, you are processing samples a few hours after installation.
Contact information
Home page: www.biosoftintegrators.com/
Email: info@biosoftintegrators.com
Phone: 619.793.5095
Address:
3755 Avocado Blvd
Suite 150
La Mesa, CA 91941
Description
DNAnexus accelerates the development and delivery of genomic medicine with a global network for sharing and managing genomic data and tools. DNAnexus provides a technology infrastructure and toolset that is optimized for addressing the challenges of security, scalability, and collaboration, for organizations that are pursuing genomic-based approaches to health in the clinic and in the research lab. The DNAnexus team is made up of experts in computational biology and cloud computing who are working with organizations to tackle some of the most exciting opportunities in human health, making it easier — and in many cases feasible — to work with genomic data. With DNAnexus, organizations can stay a step ahead in leveraging genomics to achieve their goals. The future of human health is in genomics. DNAnexus brings it all together.
Contact information
Home page: https://dnanexus.com/
Product page: https://www.dnanexus.com/product-overview
Customer support email: Support@dnanexus.com
Address:
1975 W. El Camino Real
Ste. 101
Mountain View, CA 94040
Description
Today’s next-generation sequencing environments require more computing power than ever in order to analyze enormous data sets. In fact, many core facilities have expressed concerns over their lack of computing power and storage needed. As the world’s leading provider of turn-key computing clusters for bioinformatics, PSSC Labs understands these ever-increasing requirements.
Contact information
PSSC Labs
Home page: https://www.pssclabs.com
Customer support email: 4sales@pssclabs.com
Phone: 1.949.380.7288
LIMS
Description
Exemplar is a LIMS, Electronic Lab Notebook and Data Management in a single, integrated Solution. It is highly configurable and is workflow driven to reflect how labs actually operate. Exemplar sports a fully configurable Data Model and Plugin architecture for rapid implementation in compressed time frames.
Links
Exemplar LIMS and PacBio
Specifications
Windows/Linux/OSX
MySQL or Oracle
Contact information
Sapio Sciences, LLC
Home page: www.sapiosciences.com
Email: sales@sapiosciences.com
Phone: 443.759.3204
Description
GenoLogics LIMS is one of the only full-featured LIMS built from the ground up specifically for the next-generation genomics laboratory. GenoLogics LIMS allows next-generation genomics labs and sequencing facilities to easily trace samples and project information across multiple instruments and applications, all within one centralized system. It also eliminates the informatics bottlenecks that hinder sequencing workflows and slow analysis.
Links
Additional resources
Contact information
Home page: www.genologics.com
Email: info@genologics.com
Toll-free phone: 1.866.457.5467
Main phone: 1.250.483.7011
Address:
4464 Markham Street, Suite 2302
Victoria, BC
V8Z 7X8
Genome assembly, demultiplexing + mapping
Description
Bluebee’s unique private cloud-based accelerated genomics analysis platform enables fast, efficient and affordable processing of Next Generation Sequencing data, be it for research, clinical applications, agrigenomics, or beyond. The intuitive and optimized user interface offers reliable, accessible data analysis to team members with different levels of data analysis expertise, supporting cross-functional teams with centralized sequence data analysis and storage.
Bluebee uses state-of the art data centers across The Americas, Europe, and Asia Pacific, which ensure local data processing guaranteeing compliance to both European and US standards.
Contact Information:
Website: www.bluebee.com
Email: info@bluebee.com
Phone: +31 882140200
Address:
Laan van Zuid Hoorn 57
2289 DC Rijswijk
The Netherlands
Description
DNAnexus accelerates the development and delivery of genomic medicine with a global network for sharing and managing genomic data and tools. DNAnexus provides a technology infrastructure and toolset that is optimized for addressing the challenges of security, scalability, and collaboration, for organizations that are pursuing genomic-based approaches to health in the clinic and in the research lab. The DNAnexus team is made up of experts in computational biology and cloud computing who are working with organizations to tackle some of the most exciting opportunities in human health, making it easier — and in many cases feasible — to work with genomic data. With DNAnexus, organizations can stay a step ahead in leveraging genomics to achieve their goals. The future of human health is in genomics. DNAnexus brings it all together.
Contact information
Home page: https://dnanexus.com/
Product page: https://www.dnanexus.com/product-overview
Customer support email: Support@dnanexus.com
Address:
1975 W. El Camino Real
Ste. 101
Mountain View, CA 94040
Description
Dovetail Genomics LLC provides full-service whole genome assembly for plants, animals, and microbes. Our services menu includes PacBio options for DNA extraction or QC, SMRT® library preparation and sequencing, and Falcon de novo assembly. PacBio de novo assemblies pair well with Dovetail’s proprietary Chicago™ libraries and HiRise™ scaffolding software to yield highly accurate and contiguous assemblies approaching chromosome-scale scaffolds.
Contact Information:
Services Menu: https://dovetailgenomics.com/
Email: info@dovetail-genomics.com
Phone: 831.713.4465
Description
SeqMan NGen is sequence assembly software that can assemble any size genome quickly and accurately on a desktop computer. SeqMan NGen assembles data from all major next-gen sequencing platforms and provides an extremely easy-to-use interface that steps you through your sequence assembly and analysis project. SeqMan NGen is fully integrated with Lasergene’s SeqMan Pro, so that once your assembly is complete, you can continue with downstream analysis, including discovering SNPs using Bayesian statistical models, evaluating coverage, and annotating your consensus sequence.
Links
SeqMan NGen product page
DNASTAR support for PacBio technology
PacBio assembly and analysis video
Specifications
Windows Vista x64 and Windows 7 x64
Linux Distributions: CentOS 5.5 and Ubuntu 10.04
Quad-Core 2 GHz processor
RAM requirements vary based on the type of assembly, but range from 4GB–16 GB.
Visit https://www.dnastar.com/software/molecular-biology/ for more details.
Contact information
DNASTAR, Inc.
Home page: www.dnastar.com
Email: info@dnastar.com
Phone: 608.258.7420
Toll-free in the U.S. and Canada: 866.511.5090
Call free from the U.K.: 0.808.234.1643
Call free from Germany: 0.800.182.4747
Description
Era7 offers complete microbial research solutions for de novo bacterial genomes and full-length 16S metagenomics as a research partner from start to finish. Services include Project Design, Sequencing, Assembly, Annotation and Comparative Genomics analysis solutions. With specialized in-house informatics pipelines, Era7 offers complete microbial genome annotation (BG7) and comparative analysis (CG7) systems that provide exhaustive gene prediction integrated with rich functional annotation from GO, Interpro, EC, and comparison with other reference resources with rapid turnaround time. Customizable annotation reports for specific research interests such as antibiotic resistance, membrane proteins for vaccine development, virulence genes, etc. are available. Era7 also offers full-length 16S solutions for metagenomic investigations (MG7) resulting in more specific taxonomic assignments to characterize microbial populations.
Links
de novo bacterial genomics
full-length 16S taxonomic profiling
Contact information
Era7 Bioinformatics
Website: www.era7bioinformatics.com
Email: info@era7.com
Address:
1 Broadway 14th Floor
Cambridge, MA 02142 U.S.A.
Phone number: +1(617) 401-3340
Description
Shoreline Biome’s easy-to-use companion SBanalyzer™ Software and comprehensive Athena™ Microbial Reference Database is a one-of-a-kind demultiplexing and mapping tool that simplifies and improves taxonomic assignment of data from both the Shoreline Biome V1-V9 or StrainID™ kits. Unlike software designed for use with short read 16S data, SBAnalyzer addresses both the similarities between 16S regions as well as the highly variable microbial ITS region that is essential for high resolution taxonomic assignment of microbial species and strains. This downloadable, GUI or command line software tool can be run on a laptop or server to demultiplex HiFi sequencing reads and map them to the Athena Microbial Reference Database. The curated, comprehensive Athena database lets users identify, classify and track both known and unknown microbial species and strains from even the most complex microbiome samples. Users have the option of either standard protocols or advanced protocols that leverage DADA2 to enable multi-amplicon sequence variant (ASV) fingerprinting.
Links:
Shoreline Breaker Instrument and Kits
SBanalyzer Software and Athena™ Microbial Reference Database
User Manuals and Brochures
Peer Reviewed Publications
Contact Information
Shoreline Biome
Home page: http://www.shorelinebiome.com/
Orders email: orders@shorelinebiome.com
Support email: support@shorelinebiome.com
Contact us email: hello@shorelinebiome.com
Address:
400 Farmington Ave. CB119
Farmington, CT 06032 USA
Variant detection
Description
SeqMan NGen is sequence assembly software that can assemble any size genome quickly and accurately on a desktop computer. SeqMan NGen assembles data from all major next-gen sequencing platforms and provides an extremely easy-to-use interface that steps you through your sequence assembly and analysis project. SeqMan NGen is fully integrated with Lasergene’s SeqMan Pro, so that once your assembly is complete, you can continue with downstream analysis, including discovering SNPs using Bayesian statistical models, evaluating coverage, and annotating your consensus sequence.
Links
SeqMan NGen product page
DNASTAR support for PacBio technology
PacBio assembly and analysis video
Specifications
Windows Vista x64 and Windows 7 x64
Mac OS X 10.6 or higher
Linux Distributions: CentOS 5.5 and Ubuntu 10.04
Quad-Core 2 GHz processor
RAM requirements vary based on the type of assembly, but range from 4GB–16 GB.
Visit https://www.dnastar.com/software/molecular-biology/ for more details.
Contact information
DNASTAR, Inc.
Home page: www.dnastar.com
Email: info@dnastar.com
Phone: 608.258.7420
Toll-free in the U.S. and Canada: 866.511.5090
Call free from the U.K.: 0.808.234.1643
Call free from Germany: 0.800.182.4747
Partek Flow and Partek Genomics Suite
Description
Built upon sound statistical analysis and strong visualizations, Partek Flow and Partek Genomics Suite are a user-friendly, start-to-finish software solution designed for the integration and analysis of all genomic data, from microarray through today’s most advanced sequencing technologies.
Links
Specifications
Targted Sequencing Solutions for PacBio RS Long Reads Using Partek Flow and Partek Genomics Suite
Partek Flow brochure
Partek Genomic Suite brochure
Contact information
Partek Incorporated
Home page: www.partek.com
Email: inquire@partek.com
Phone: 314.878.2329
Description
CLC Genomics Workbench and CLC Genomics Server provides a framework for visualizing, combining, and analyzing whole-genome data. The framework enables user-friendly comparative filtering of genomic variations, giving scientists a quick and easy way to do functional classification and filtering of SNPs and other kind of genomic variations, using multiple data sources including Ensembl, UCSC, and other external public databases. This framework offers you an intuitive way to do further downstream analyses and to combine them with existing knowledge.
Links
Description and video
Application note
Specifications
Specifications
Contact information
Phone EMEA: +45.7022.5509
Phone Americas: +1.617.945.0178
Phone AsiaPac: +886.2.2790.0799
Main email: info@clcbio.com
Support email: support@clcbio.com
Sales email: sales@clcbio.com
Address:
CLC bio
Finlandsgade 10
Katrinebjerg
8200 Aarhus N
Denmark
Description
SNP & Variation Suite 7 is an integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data. SVS was created specifically to empower biologists and other researchers to easily perform complex analyses and visualizations, eliminating the need to rely exclusively on bioinformatics experts or cobble together difficult-to-use, incompatible freeware. With SVS, you can focus on your research instead of learning to be a programmer or waiting in line for bioinformaticians.
Links
Golden Helix and PacBio video
Specifications
Windows, Linux, or Mac (32 and 64-bit). No special memory or processor requirements, but the larger your study, the more you need. Here is a link to where we talk about this.
Contact information
Home page: www.goldenhelix.com
Blog: http://blog.goldenhelix.com
Phone: 406.585.8137 or 888.589.4629
Address:
203 Enterprise Blvd
Suite One
Bozeman, MT 59715
Tertiary analysis
Description
CLC Genomics Workbench and CLC Genomics Server provide a framework for visualizing, combining, and analyzing whole genome data. The framework enables user-friendly comparative filtering of genomic variations, giving scientists a quick and easy way to do functional classification and filtering of SNPs and other kind of genomic variations, using multiple data sources including Ensembl, UCSC, and other external public databases. This framework offers you an intuitive way to do further downstream analyses and to combine them with existing knowledge.
Links
Description and video
Application note
Specifications
Specifications
Contact information
Phone EMEA: +45.7022.5509
Phone Americas: +1.617.945.0178
Phone AsiaPac: +886.2.2790.0799
Main: info@clcbio.com
Support: support@clcbio.com
Sales: sales@clcbio.com
Address:
CLC bio
Finlandsgade 10
Katrinebjerg
8200 Aarhus N
Denmark
Description
Era7 offers complete microbial research solutions for de novo bacterial genomes and full-length 16S metagenomics as a research partner from start to finish. Services include Project Design, Sequencing, Assembly, Annotation and Comparative Genomics analysis solutions. With specialized in-house informatics pipelines, Era7 offers complete microbial genome annotation (BG7) and comparative analysis (CG7) systems that provide exhaustive gene prediction integrated with rich functional annotation from GO, Interpro, EC, and comparison with other reference resources with rapid turnaround time. Customizable annotation reports for specific research interests such as antibiotic resistance, membrane proteins for vaccine development, virulence genes, etc. are available. Era7 also offers full-length 16S solutions for metagenomic investigations (MG7) resulting in more specific taxonomic assignments to characterize microbial populations.
Links
de novo bacterial genomics
full-length 16S taxonomic profiling
Contact information
Era7 Bioinformatics
www.era7bioinformatics.com
info@era7.com
1 Broadway 14th Floor
Cambridge, MA 02142 U.S.A.
Phone number: +1(617) 401-3340
Description
SNP & Variation Suite 7 is an integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data. SVS was created specifically to empower biologists and other researchers to easily perform complex analyses and visualizations, eliminating the need to rely exclusively on bioinformatics experts or cobble together difficult-to-use, incompatible freeware. With SVS, you can focus on your research instead of learning to be a programmer or waiting in line for bioinformaticians.
Links
Golden Helix and PacBio video
Specifications
Windows, Linux, or Mac (32 and 64-bit). No special memory or processor requirements, but the larger your study, the more you need. Here is a link to where we talk about this.
Contact information
Home page: www.goldenhelix.com
Blog: http://blog.goldenhelix.com
Phone: 406.585.8137 or 888.589.4629
Address:
203 Enterprise Blvd
Suite One
Bozeman, MT 59715
Description
Now you can amplify highly polymorphic HLA genes with confidence and analyze both alleles using the PacBio System. The product line includes HLA Class I and HLA Class II typing kits. Whole HLA genes are amplified with NGSgo‐AmpX amplification primers in a single reaction using QIAGEN LongRange polymerase. DNA template prep and related sequencing reagents are purchased directly from PacBio. The amplicons generated by the NGSgo‐AmpX kit are ready to go directly into SMRTbell library preparation and subsequent SMRT Sequencing. The resulting PacBio consensus sequences are fully compatible with the NGSengine analysis software.
Contact information
Genome Diagnostics B.V.
Home page: https://www.gendx.com/home
Product page: https://www.gendx.com/pacbio-ngs
Customer support phone: +31.0.30.252.3799
Customer support email: support@gendx.com
Data analysis services
Description
Computomics is a team of world-leading experts in plant research and bioinformatics, offering next-generation sequencing (NGS) analyses for agriculture biotech companies and crop scientists. Whether you are concerned with crop improvement, seed production, or plant protection, Computomics helps navigate the complexities of grain, vegetable, fruit, and other genomes. Our advanced bioinformatics services provide our customers with quality NGS data interpretation from state-of-the-art genomics tools and technologies. Let us help you achieve your research goals.
Contact information
Home page: https://www.computomics.com/index.php/company.html
Product page: https://www.computomics.com/
Customer support phone: +49.7071.568.3995
Customer support email: info@computomics.com
Address:
Computomics GmbH & Co. KG
Sand 14
72076 Tübingen
Germany
Description
CosmosID is a microbial genomics platform focused on rapid characterization of microorganisms, pathogens and
anti-microbial resistance for infectious disease identification, food safety inspections, pharmaceutical discovery, public health surveillance and microbiome analysis.
Contact information
CosmosID, Inc.
Home page: https://www.cosmosid.com/
Services page: https://www.cosmosid.com/nextgeneration-sequencing
Web app: app.cosmosid.com
Customer support email: info@cosmosid.com
