We are pleased to announce that PetaGene has signed an agreement appointing Dubai based Alliance Global (AGBL) as the exclusive distributor of our genomic data management software in Middle East, Africa, Central Asia, Pakistan, Bangladesh and Sri Lanka.
The number of national population-scale genomics initiatives in the region is growing and AGBL is a leading distributor of Illumina sequencing technology in the region
“AGBL already possesses significant expertise in sequencing technology sales and the wider genomics marketplace, making it an ideal partner for us in this region,” commented Vaughan Wittorff, Ph.D., Cofounder and Chief Commercial Officer of PetaGene. “We are excited to be working with AGBL to bring PetaGene’s software to genomics researchers across Africa, the Middle East and Asia, so that they can access their genomic data faster, more efficiently, and store it more cost-effectively.”
PetaGene’s compression software, called PetaSuite, addresses challenges caused by growing volumes of genomics data. It achieves savings of between 60 and 90 percent in both storage costs and data transfer times compared to BAM and gzipped FASTQ files. PetaSuite transparently integrates with existing storage infrastructure and bioinformatics pipelines, and PetaSuite Cloud Edition enables a user’s software tools and pipelines to seamlessly integrate with a wide variety of cloud platforms without modification.
Speaking for AGBL, Group Commercial Director, Dr. Nassim-Marie Hambouz said, “We are delighted to add PetaGene to our portfolio of partners. Their innovative technology will help organizations optimise their on-site or cloud storage costs for the growing volume of genomic data throughout the region.
PetaGene will be attending the Biodata World Congress in Basel, Switzerland from 4th to 5th December.. It’s a great opportunity to meet and tell us about the challenges you face when storing and working with NGS genomic data.
Come along to discuss how our dramatic compression ratios, combined with the right storage architecture, can help you substantially reduce your storage costs, speed up transfer of genomic data; and enable collaboration through the cloud.
PetaGene’s PetaSuite compression software and cloud-computing solutions speed up data transfers and reduce storage costs for research projects involving genomics data.
We are pleased to announce that Astrazeneca has selected PetaSuite software to compress the genomics data sets for AstraZeneca’s Centre for Genomics Research (CGR). Using genomics data and state-of-the-art methods for genomic analysis, the CGR investigates underlying genetic causes of disease and aims to integrate genomics across the company’s drug discovery platform. PetaSuite accelerates data transfers for cloud computing and reduces storage costs for any research project involving genomics data.
“Using genomic data for biopharmaceutical targets discovery requires large cohorts with massive multi-petabyte data sets. The time required to transfer these data from sequencers to compute clusters as well as the cost of storage can cripple these large initiatives,” said Vaughan Wittorff, Ph.D., Co-founder and Chief Commercial Officer of PetaGene. “PetaSuite addresses the challenges caused by growing volumes of genomics data and achieves up to 10x reductions in storage costs and transfer times, while adhering to the industry-standard BAM and FASTQ genomics file formats.”
More than 200,000 files processed
To date, AstraZeneca’s CGR has processed more than 200,000 genomics datasets, generating over a petabyte of data. One petabyte of data is equivalent to streaming HD movies for 40 years without a break. At this volume of data, problems in processing time, data transfers and storage size can impact the ability to deliver at scale. PetaGene’s compression software will enable the CGR to compress over 200,000 BAM files in a 24-hour period and will add the compressed data to tiered cloud storage.
Average data size reduction of 76%
“AstraZeneca’s Centre for Genomics Research has the bold ambition to analyse up to two million genomes by 2026. Minimizing the storage footprint and transfer time of genome data while maximizing data access and compute processing is a necessity to enable us to achieve our ambition.” said Slavé Petrovski, Vice President and Head of Genome Analytics and Bioinformatics, Discovery Sciences, R&D, AstraZeneca.
PetaSuite will enable the CGR to achieve an average data reduction of 76% or a 4x expansion of storage capacity. PetaGene’s transparent, lossless compression of files reduces transfer times to less than a quarter, and PetaGene’s software allows unmodified analysis tools to run more quickly.
PetaSuite users typically make it an intrinsic part of their cloud or locally hosted analysis pipeline. As data is processed, it is compressed ready for use in the next stage of analysis without it needing to be decompressed later. PetaSuite Cloud Edition allows for the seamless integration of an organization’s own tools and pipelines in the cloud or local environment of their choosing.
Click here to read the far-reaching GenomeWeb article of 31st October 2019 about PetaGene which includes this news about AstraZeneca (requires premium subscription).
We are pleased to announce that Princess Máxima Center for Pediatric Oncology, the largest pediatric cancer center in Europe, has chosen to use PetaGene’s transparent, lossless genomic data compression software, called PetaSuite, to reduce its data storage costs while accelerating access to the data. Next-generation sequencing plays an integral role in the Center’s diagnostics and research discoveries. These valuable genomic datasets are large, and their volumes are growing. As such the Center sought to find a compression technology that can store genomic data for longer at a much lower cost while removing bottlenecks in genomic sequence analysis.
PetaGene’s PetaSuite software was evaluated by the Center against other compression techniques and unlike these, PetaSuite met and exceeded the criteria for a simple to implement and high compression performance solution, supported to a commercial standard.
Positive evaluation results
Senior Principal Investigator Dr. Patrick Kemmeren at the Princess Máxima Center describing the process, said: “Our tests with PetaGene’s compression software gave very positive results. We tested whole exome samples, RNA-Seq and whole genome sequencing data for different tumor samples. Implementing the software on our high-performance compute cluster is easy, the compression ratios are larger than what we obtain compared to CRAM compression, and accessing data is actually slightly faster compared to non-compressed BAM files. This on top of the added benefits of not having to switch to a different file format, a perpetual license for decompression and the time gains in not doing the BAM to CRAM conversion/retooling (and vice versa for some tools). As a result, we decided to implement PetaGene’s compression software within our computational infrastructure.
The right software at the right time
Jos Leendertse, Manager Research IDT at Princess Máxima Center, commented “By implementing PetaGene’s compression software we are also able to speed up the migration process to our new storage infrastructure. It’s not only the right software but also at the right time.”
Vaughan Wittorff, Ph.D., Cofounder and Chief Commercial Officer at PetaGene added, “During the evaluation process, the researchers found PetaSuite’s transparent access technology particularly compelling since it meant that the compressed data could integrate seamlessly with the bioinformatics structure Princess Máxima Center’s already had in place. A key challenge with compression is to ensure that end-users can continue working with the compressed files without having to change their existing, optimised workflows. PetaGene has solved this by ensuring that the compressed files are readable to existing tools and pipelines in the compressed state. This means our customers do not have to change any of their tools and pipelines, making it easy to integrate our compression technology within their infrastructure.”
About Princess Máxima Center for Pediatric Oncology
Opened in 2018, the Princess Máxima Center for Pediatric Oncology, based in Utrecht, The Netherlands, consolidated the work of seven different academic centers across the Netherlands into the largest pediatric cancer center in Europe. As both a hospital and a research institute, the Center has a combination of world-class facilities, leading clinicians and researchers all driven by a passion to cure pediatric cancers. By integrating the research facilities with the hospital, the Center is better equipped to implement novel discoveries into clinical care. For more information, visit www.prinsesmaximacentrum.nl/en.
We are pleased to announce that PetaGene has signed an agreement appointing Genique Lifesciences as the exclusive distributor of our genomic data management software in India.
The agreement will allow India-based Genique Lifesciences to act as the exclusive sales channel for PetaGene’s genomic data compression software for the growing Indian market. Genique’s founding team has extensive experience with distribution of Next Generation sequencers in India.
“Genique already possesses significant expertise in sequencing technology sales and the consumer DNA testing market, making it an ideal partner for us in India, one of the fastest growing genomics markets,” commented Vaughan Wittorff, Ph.D., Cofounder and Chief Commercial Officer of PetaGene. “We are excited to be working with Genique to bring PetaGene’s software to genomics researchers in India, so that they can access their genomic data faster, more efficiently, and store it more cost-effectively.”
Speaking for Genique Lifesciences, Cofounder and CEO, Abhishek Das said, “We are delighted to represent PetaGene in India. Their innovative technology will help organisations optimise their on-site or cloud storage costs for the growing volume of genomic data in India.”
Significant developments in India include the Department of Biotechnology launching the Genome India project later this year with the target of sequencing the genome of 10,000 Indian citizens.
One year ago, Frontline Genomics published Genomic Data 101, its guide to the technology and hardware landscape for genomic data storage and analysis. It proved a valuable primer for anyone looking to find out about compression and general management of genomic data.
The data infrastructure to support genomic research, including compression, has evolved since the original guide. Frontline Genomics have published a new version. It’s called Biodata Analysis and Management – Genome Analytics, Interoperability, and Data Life Cycle.
The new publication addresses key issues:
The landscape of compression options and the enhanced benefits of techniques developed specifically for genomics.
The state of the art.
Technical considerations when choosing a compression solution.
Commercial considerations – ROI.
Specific considerations when storing data in the cloud
How different compression techniques integrate with existing and new analysis workflows.
There is new information on the innovations and developments in genomic compression, which include:
The improved compression ratios now being achieved.
Data to show how efficient commercially available compression gives better savings than would be obtained using a free open source tool.
How the plateauing of storage costs mean it’s no longer possible to rely on the historical trend for reductions in storage costs.
You can download the paper here to discover the latest on compression and other aspects of genomic data management.
The latest addition to our product range, PetaSuite Protect, won “Best of Show” earlier this month at BioIT World Conference & Expo 2019, the premier conference for IT in Life Sciences. This is our third “Best of Show” win, previously winning in 2016 and 2018. This year, 31 new products were considered by an expert panel of judges who awarded PetaSuite Protect the ‘Nailed It’ award.
In the award citation, Phillips Kuhl, President at Cambridge Healthtech Institute said, “Our judges believe this is a new, powerful and highly relevant approach to security, driven by a passionate and invested team”.
PetaSuite Protect provides users with the tools to encrypt their genomic data; manage fine-grain access to it, and demonstrate compliance with applicable regulations. As with the established PetaSuite compression technology, the new encryption and access capabilities are completely transparent to genomic tools and analysis pipelines.
Dan Greenfield, our co-founder and CEO said, “We’re thrilled to win this illustrious award for the third time. We’re particularly grateful to the judges for recognizing the relevance of our approach to this important element of genomic data management.”
To find out more about PetaSuite Protect please get in touch via our contact us page.
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Would you like to join a funded, award-winning and growing Cambridge start-up working in the increasingly vital field of genomic data?
We are looking for developers and a business support administrator.For the developer roles you’ll need to be proficient in C/C++ and it would help if you’re comfortable working with algorithms.
For the business support administrator position, we’re looking for someone with experience in a business support role. You will need to be well-organised, persistent and accurate to help make our sales operation as effective as possible.
Every year the ASHG annual meeting attracts the thought leaders in the field of human genetics. Will you be among them at ASHG 2018 in San Diego? If so, visit us on booth #819 during the three days of the exhibition, October 17th to 19th, to let us know about the data challenges you face.
Our team has extensive experience in health information technologies, systems development and large-scale genomics. We’ll be delighted to discuss how to address the frustrations caused by ever increasing volumes of genomic data.
Those challenges go beyond the simple cost of on-premises or cloud storage. There’s the transfer and analysis times for large data sets to consider too. Speeding those up can give a great boost to your research. Our PetaSuite compression software integrates seamlessly with analysis pipelines, reduces I/O demand and facilitates collaboration.
We’ll also be hosting a session in CoLab Theater 3 on Thursday 18th from 4:00 to 4:15pm to present on how using appropriate compression technology can benefit commercial and research organizations working with genomic data.
If you’re attending ASHG 2018 in San Diego, drop by booth #819 or book a meeting in advance of the show to make sure we fit into your schedule. We look forward to seeing you there.
If you’d like to know more about the ASHG meeting or register to attend, visit the website.
We launched PetaSuite Cloud Edition (CE) at Bio-IT World 2018, the premiere conference for IT in the Life Sciences. Its benefits for organisations working with genomic data in terms of reduced storage cost, shorter data transfer times and quicker analysis were immediately recognised by the judges of the Best in Show awards; they awarded it top prize in the storage infrastructure and hardware category. This is the second time we have won this influential award. The original version of PetaSuite picked up Best of Show in the category for optimising speed and storage at the same event in 2016.
In her award citation for PetaSuite CE, Allison Proffit, Bio-IT World Editor, said: “the judges were very impressed with an offering that lets users access data compression, objects in storage or an s3 bucket, all from the command line.”
Petasuite CE allows a user’s software tools and next generation sequencing (NGS) pipelines to seamlessly integrate with a wide variety of cloud storage platforms without modification. Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform (GCP), private cloud and hybrid cloud are all supported transparently.
PetaSuite CE also delivers significantly improved, high-performance, scalable genomic compression technology. Lossless compression ratios of up to 10x for GATK BAM files are now possible. Other NGS file types such as FASTQ.gz can now also achieve much better compression ratios. For FASTQ.gz files, the ratio is up to 4.3 times compression. This represents a potential space saving of 77%, which brings dramatic cost and transfer time reductions without compromising the quality of the original genomic data.
Dan Greenfield, our co-founder and CEO said: “We are honoured to win this prestigious award for the second time. The fact that the judges acknowledged the importance of our seamless cloud integration, with its implications for scaling and collaboration, was particularly pleasing. We will continue to strive to create solutions which speed up cooperation and analysis for our research and diagnostic customers.”
Find out more about PetaSuite Cloud Edition on the products page or get in touch via our contact page.