Nanopore service providers update: three new providers, and more

KeyGene

KeyGene is the go-to AgBiotech company for higher crop yield & quality. Our goal is to help organizations with their toughest R&D challenges, combining our cutting edge breeding technologies, bioinformatics & data science expertise and plant-based trait platforms.

KeyGene has always been frontrunner in the application of new sequencing technologies for crop improvement and believes that long reads are crucial to generate high-quality reference genomes. Since its introduction in 2014, KeyGene used ONT’s MinION to sequence plant pathogens, BACs, amplicons and complex crop genomes. Also the ability to directly sequence RNA will disrupt the current short-read oriented field and enable many new applications.

KeyGene is excited about the ability to sequence truly complex plant genomes with Oxford Nanopore’s platforms in just a few days. De novo whole genome sequencing and analysis will be the standard going forward.

Interested to hear more about KeyGene’s achievements on nanopore sequencing? We will present our latest results on sequencing and assembly of lettuce genomes at the London Calling conference in May. Hope to see you in London!

Microbes NG

We are really excited to be certified as a Service Provider for Oxford Nanopore sequencing. MicrobesNG is a microbial sequencing service that provides genomes for the microbial community. Incorporating Oxford Nanopore technology into our service options allows us to provide a new enhanced genome service to our customers that delivers top quality genome assemblies for challenging microbial applications. These assemblies take advantage of the long reads obtained with Oxford Nanopore technology to bridge over repeat regions, vastly improving the structure of the assembly.

We are looking forward to advancing our enhanced genome service, if you would like more information please contact us.

Sequencing Platform of I2BC

As one of few Nanopore service providers based in France, the Sequencing Platform of I2BC offers a variety of sequence services as well as bioinformatic analyses.

BaseClear & Future Genomics Technologies

In 2017 BaseClear and Future Genomics Technologies became the first certified service provider of Oxford Nanopore Technologies. We have supported a wide range of projects, including structural analysis of synthetic DNA constructs, the rapid assembly of complex microbial genomes as well as large animal genomes and the ultra-large tulip genome. We also offer metagenomics analysis of complex environmental samples. We work with researchers mainly from Western Europe and offer complete genomics services including sampling, extraction, library preparation, sequencing and analysis. BaseClear and Future Genomics Technologies also provide consultancy and support for project design, particularly useful if you are new to Oxford Nanopore technology.

University of Illinois at Urbana-Champaign

The DNA Services unit of the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, one of the first Oxford Nanopore Certified Service Providers to offer sequencing with the GridION, has been consistently achieving complete de novo assembly of microbial genomes into one scaffold, as well as the full assembly of all their associated plasmids. The high output and long reads obtained with the 1D libraries enable full assembly of up to 10 microbial genomes per flow cell, bringing the cost of microbial assembly to a few hundreds of dollars. A low coverage of short reads is used to correct indels that remain after polishing of the Oxford Nanopore assembly. The technology has also enabled the facility to fully sequence the genomes of several fungi. It is currently being used to assemble the genomes of several nematodes and also to generate long reads for eukaryotic species with large genomes, to provide more contiguity to existing assemblies.

Additionally, we have been performing full length cDNA sequencing, which has enabled a more thorough characterization of splicing variants in RNA samples than what can be obtained with short reads. An application that is being developed and had produced strong preliminary results in the sequencing of full-length 16S rRNA amplicons constructed with the Fluidigm system. This application yields millions of reads per run and the reads can be easily demultiplexed and analyzed using the publicly available software.

Garvan Institute of Medical Research

Six internal research groups, as well as a dozen external groups, have begun working with the Garvan Institute of Medical Research’s nanopore sequencing facilities.

This work has been related to many disease areas including cancer, neurology, immunology and pathogen identification.

Garvan has performed nanopore sequencing runs related to structural variants and DNA methylation, and done ultra long reads and direct RNA sequencing.

Genome Transcriptome Facility of Bordeaux

The Genome Transcriptome Facility of Bordeaux has been a Nanopore certified service provider since 19th February 2018, for both DNA and RNA. We have carried out research projects on various applications including:

• de novo sequencing on bacteria, bacteriophage, fungi, tomato, stevia, oak.
• Amplicon sequencing (15kb long range PCR) for detection of large deletions in human mitochondrial genome.
• 16S analysis of leaf, insect and human microbiote

We look forward to hearing from you

NextOmics, a GrandOmics company

NextOmics, based in China, is providing nanopore sequencing as a service to people across the region, for human, plant, animal and microbial genomics.

GrandOmics, the parent company of NextOmics, has recently launched the Personal Reference Genome Project, which will provide a ‘platinum de novo personal genome’ to customers. The PRGP aims to provide 10K samples in the first 2-3 years and 10 million in the following years.

Read more about the project here: http://www.grandomics.com/PRGSP/

De Novo Genomics

De Novo Genomics was the first US based certified Oxford Nanopore service provider. Since our certification, we have been providing nanopore sequencing service to researchers from all over the world. It has been exciting for us to see the breadth of species diversity in the sequencing projects we are supporting. From flowers and flies, to coffee and primates, researchers are keen on leveraging nanopore technology for whole genome and transcriptome sequencing.

Beyond our sequencing services we have been involved in several research collaborations. A transcription factor project has allowed us to demonstrate the usefulness of nanopore sequencing for ChIP-seq. In some situations we recovered enough material to allow the sequencing of non-amplified libraries. For another project we were assessing the splicing fidelity of transcripts generated from a human disease associated gene. Nanopore sequencing revealed that, for some patients, numerous novel splice isoforms are generated resulting in premature stop codons. One of our more interesting and challenging collaborations has been looking at RNA modifications in reproductive tissue. This collaboration has made us very excited about the use of nanopore sequencing for studying both RNA and DNA base modifications.

We have enjoyed working with researchers to help them leverage Oxford Nanopore sequencing technology from both a service perspective and from more in depth collaborative research projects. Our work has allowed us to develop expertise in a wide range of services that include and are not limited to: whole genome, transcriptome, immunoprecipitation, and target amplicon sequencing. We look forward to continuing our support of researchers in their pursuit of discovery.

Follow us on twitter (@DeNovoGenomics) to get updates on developments or find our contact details via the following link.

Takara Bio Inc.

Takara Bio offers Oxford Nanopore long reads sequence and data analysis services combining our long experience as a sequence service provider.

With advent of next generation sequencing technologies, more organisms including microbes, plants and human are possible to be analyzed and its applications are expanding. We have set up numerous sequencers with high-speed data analysis server accommodating a variety of analysis needs. Oxford Nanopore GridION will help to tackle with non-model organism genome and complex genetics analysis. Our biggest data analysis environment in Japan and long term experienced analysis methods will support your research.

GeneBay

We have recently launched an unprecedented service that can deliver near complete microbial genome assemblies taking full advantage of the Oxford Nanopore system. Since then, we have a growing number of potential customers from bacterial genomics community, who wish to have high quality genome sequences in a rapid and cost-efficient manner.

Not only the assembly of small bacterial genomes, but we also see success in assembling larger eukaryotic genomes such as fungi and plants. With these progress, we can now provide high quality de novo assembled genomes using Oxford Nanopore long reads from a variety of organisms such as bacteria, animals and plants.

As a sequencing service provider, we can provide sequencing runs flexible to customers' specific needs. We can provide sequencing runs favorable to longer read length or higher throughput settings depending on requests. We can accommodate with multiplexing samples in a single flowcell and other analysis as well.

Our long bioinformatics experience will help and guide you to the success of long reads analysis.