“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.
About PetaGene
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 sales@petagene.com.
