Posted on October 8, 2020
Genome UK is an exciting and ambitious new strategy that builds upon the UK’s world-leading excellence in genomics to build “the most advanced genomic healthcare system in the world”. We applaud this initiative, and believe this will enable the NHS to leverage precision medicine to improve outcomes and reduce costs, significantly drive research into new treatments and diagnostics, as well as foster an ecosystem for the UK Genomics Industry to thrive.
However, this is all contingent on getting the execution right, and we have seen past ambitious genomics projects suffer due to what are “Bio-IT” issues, that is IT problems with practically handling biological datasets. Due to the scope of this initiative, and having had a great deal of experience addressing issues in this domain, we have some recommendations for how to prevent some foreseeable problems, and to make it a real success.
Our recommendations cover key issues in:
- data security and privacy, including regional encryption and data minimisation
- reducing technical barriers to ensure efficient IT and lower costs
- the need for computational reproducibility, and supporting existing pipelines
- data integrity and information loss
Click here to download the 7-page slide deck.
Posted on October 6, 2020
PetaGene and NVIDIA announce seamless integration of PetaGene’s PetaSuite tools as a standard part of NVIDIA Clara Parabricks Pipelines. PetaGene’s transparent compression reduces file sizes by 60-90%, and enables Parabricks Pipelines GPU-accelerated genome analysis to run 29% faster.
Cambridge, UK, Oct. 6, 2020: PetaGene and NVIDIA today announce their integrated bioinformatics solution to accelerate genomic analysis and simultaneously reduce data storage. PetaGene’s PetaSuite software decreases the size of genomic data and is integrated into NVIDIA Clara™ Parabricks Pipelines, a GPU-accelerated tool for accurate genomic data analysis. This technology combination now allows scientists and clinicians to access PetaGene’s genomic compression software within Parabricks Pipelines compute framework. FASTQ.gz and BAM files compressed by PetaGene’s PetaSuite software within Parabricks Pipelines compute framework or elsewhere can now be analyzed directly with Parabricks Pipelines.
PetaGene and Parabricks clear choices for TGen
The Translational Genomics Research Institute (TGen), a nonprofit medical research institute that is examining the genetic components of common and complex diseases, has confirmed faster end-to-end analysis when using PetaGene-compressed files within Parabricks Pipelines. TGen confirmed that the transparent readback of the compressed files using PetaGene’s user-mode library is now fully compatible with the Parabricks Pipelines environment. Sequencing and compute costs have plummeted, but storage costs have not. With Petagene and GPU-powered Parabricks Pipelines, genomic analyses can be run faster, and with significant cost savings on storage and compute.
“At TGen, we have a long history of working with a large number of bulky genomic files. As our workflows mature and scale, we have been keen to build our genomics infrastructure from the ground up with the most efficient tools and systems available.” said Dr Glen Otero, VP of Scientific Computing at TGen. “PetaGene and NVIDIA Clara Parabricks Pipelines were independently clear choices for us. Having them interoperable like this is important, and the fact that the combination further accelerates the aggregate performance is fantastic.”
PetaGene gives 29% speedup to Parabricks Pipelines without added complexity
TGen’s benchmarking showed that germline workflows in Parabricks Pipelines run 29% faster with PetaGene-compressed data than with regular genomics files, and generate identical results. This significant speedup is due to the behind-the-scenes I/O savings from PetaGene’s PetaLink user-mode library as it does just-in-time decompression. Since this library creates virtual FASTQ.gz and BAM files, users of the compressed files never need to interact directly with the compressed files – the virtual files are fully compatible with all existing tools and pipelines. Besides PetaGene’s compressed data, Parabricks GPU-accelerated analysis workflow is a clear differentiator compared to CPU-based workflows. GPUs save on overall space and operational costs as it requires fewer GPU servers than CPU servers to run the same analyses.
NVIDIA Clara Parabricks Product Manager Tim Harkins, Ph.D. commented, “Many scientists and clinicians are working hard to identify those genetic variants that contribute to health and diseases, ultimately providing better therapeutic choices for patients. The amount of data generated on a per individual genome is significant and all trends are pointing to more growth. The compression technologies from Petagene are going to save the community a significant amount in data storage, and by integrating with Parabricks Pipelines, the amount of time saved will be of an equal contribution.”
Dr Vaughan Wittorff, Co-Founder and Chief Commercial Officer of PetaGene said: “GPU-Powered NVIDIA Clara Parabricks Pipelines appeals to customers who want the fastest analysis speeds for genomics, and those kinds of customers also want the most efficient storage techniques without having to change anything they do and without vendor lock-in. Integrating PetaGene tools with NVIDIA’s genomic tools was therefore very natural. The fact that PetaGene’s transparent compression also makes Clara Parabricks even faster is great for everyone.”
Joint free trial of Parabricks and PetaGene available today
Get Started today. NVIDIA and PetaGene provide a FREE 30-day license to NVIDIA Clara Parabricks which comes with a free trial of PetaGene’s PetaSuite tools to do compression and transparent readback.
PetaGene was founded in Cambridge, the birthplace of genomics, to address the rapidly growing data management problems of the genomics industry. PetaGene’s software enables compression of huge amounts of genomic data without compromising on access or data quality. The company’s products go beyond regular data reduction techniques and have three times been recognized by Bio-IT World’s Best of Show Award for their industry-leading performance and usability. For more information visit https://petagene.com or e-mail firstname.lastname@example.org.
Posted on January 24, 2020
Genomic data files, whether BAM or FASTQ.gz format, are large and make huge demands on IT infrastructure. But, how can you tell if the challenges you face can be solved by compressing your genomic data with PetaGene technology? Here’s a list of six scenarios where lossless compression with transparent read-back will help.
1. Your storage systems are nearing capacity
PetaGene compression transparently multiplies your existing storage capacity by between 2.5x and 11x. You don’t need any scratch space when using the compressed data.
2. You want to move data to public clouds
PetaGene tools allow painless bulk or incremental migration to the cloud, and compressed data can be randomly accessed and streamed directly from object storage as if they were regular files.
3. Your cloud storage/egress bills are out of control
PetaGene compression will reduce both of these bills by 60-91%.
4. You need to archive data but want to maintain access
With PetaGene compression you can keep all your data in hot storage, for the same overall cost as keeping it uncompressed in cold storage and accessing it infrequently.
5. Data transfers are a bottleneck to your analysis pipelines
When your pipelines are I/O bound, PetaGene compression typically speeds them up by 2-3x.
6. You would like to recover budget from storage for more research
If you are experiencing any of these issues, just hit the ‘Free trial’ button at the top of this page to ask for a free Software Evaluation package, or click here.
Posted on October 24, 2019
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).
Posted on October 22, 2019
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 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.
Posted on October 3, 2019
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.
To contact Genique, visit their website.