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Aldec and Indian Institute of Science faculty enterprise, ReneLife, showcase ReneGENE for accurate genome alignment on HES Accelerator at SC16

Date: Nov 14, 2016Type: Release

Henderson, NV – November 14, 2016 - Aldec, Inc., a pioneer in mixed-HDL language simulation and hardware-assisted verification solutions for FPGAs and ASICs and ReneLife Private Limited, a faculty enterprise of the Indian Institute of Science (IISc), Bangalore, India proudly announce and showcase their joint effort in establishing an accelerator platform that implements ReneLife’s proprietary core technology, ReneGENE. The solution performs ultra-fast and accurate big data mapping and alignment of DNA short-reads on large reference genomes using Aldec’s high quality HES-HPC™ FPGA-based Accelerator, and will be demonstrated at SC16, the International Conference for High Performance Computing, Networking, Storage and Analysis (Booth# 4476) to be held in Salt Lake City, Utah, November 14-17, 2016.

 

About ReneGENE

  • Proprietary core technology, offered on HES-HPC™ as AccuRA, for accurate, and ultra-fast big data mapping and alignment of DNA short-reads from the Next Generation Sequencing (NGS) platforms, with full coverage of the genome (million to billion bases long), including repeat regions
  • Fully streaming, multithreaded, parallel dynamic programming in hardware eliminates memory bottleneck and storage issues
  • Reduces computing and I/O burden on the host significantly
  • Scalable and massively parallel computing and data pipeline
  • Achieves short read mapping in minimum deterministic time

 

ReneGENE Performance

  • AccuRA scales well on the Aldec HES-HPC™ platform, at multiple levels of design granularity
  • Alignment time is ~10x faster than GMAccS, the single GPU OpenCL implementation of ReneGENE. GMAccS itself qualifies to be ~2.62x faster than CUSHAW, the open source single GPU CUDA implementation
  • With GMAccS itself demonstrating a speedup of over 150x compared to standard heuristic aligners in the market like BFAST, AccuRA is several orders faster than the competitors, offering accuracy over heuristics.

 

To align 500 million reads (100 bases long) against the reference genome (3 billion bases long), with each read reporting a mapping at five locations on the reference, AccuRA performs 4.65 Tera map operations and 10.24 Tera cell updates at the rate of 21.14 GMPS (Giga Maps Per Second) and 46.56 GCUPS (Giga Cell Updates per Second) in about 3.66 minutes, with data streamed in over the PCIe interface.

 

“SC-16 presents a wonderful opportunity to showcase the capabilities of ReneGENE. With a multi-FPGA environment in the offering on Aldec boards, we will scale the performance further in order to get full alignment in seconds,” said Santhi Natarajan, Research Associate, Indian Institute of Science.

 

“AccuRA successfully handles genomes of sizes ranging from millions to billions. With a single FPGA on the HES-7 platform, AccuRA has successfully aligned about 650 GB of human genome short read data sets in just a few minutes. We owe it to Aldec’s professional RTL Porting Services extended by Aldec technical team towards this effort,” said Professor Debnath Pal, co-founder of ReneLife.

 

“The cooperation with ReneLife is a great example of how science and industry can bring to life new solutions for genome analysis integrating the power of ReneGENE and speed of Aldec HES-HPC technology,” said Zibi Zalewski, General Manager, Aldec Hardware Division. “The main challenge was to have the most optimal porting of AccuRA into the FPGA resource with the highest possible speed of host-to-FPGA transmission and an ease of integration which was realized using our Proto-AXI interface available with our HES accelerator boards.”

 

“AccuRA is several orders faster than its competitors. ReneGENE is an affordable solution, deployable both in cloud and local platforms, and is pluggable to any genome analysis pipeline for use across multiple domains from research to clinical environment,” said Professor S K Nandy, co-founder of ReneLife.

 

“Aldec’s RTL Porting Services is based on 30+ years of experience and expertise in FPGA/ASIC development, hardware programming languages and verification methodologies,” said Louie De Luna, Aldec Director of Marketing. “We believe that RTL Porting Services is critical for successful deployments of High Performance Computing (HPC) algorithms and applications. Scientists and software engineers need a ready-to-use FPGA-based accelerator without low level hardware integration implications. Understanding such a use model, Aldec provides HPC turnkey solutions that include FPGA-based Accelerators and RTL Porting Services with a complete software stack that includes PCI Express driver and software API that is easy to use and available for both Linux and Windows hosts.”

 

Visit Aldec.com to download the datasheet about ReneGENE running on the Aldec HES platform.

 

About ReneLife

ReneLife is a technology start-up, launched as a faculty enterprise of the Indian Institute of Science, in the area of Life Sciences. ReneLife is devoted to providing cutting-edge hardware-software co-designed accelerated solutions. It has made a start by developing ReneGENE - a proprietary core technology, for accelerated accurate alignment of short reads from NGS platforms through massively parallel and scalable realizations. The objective of the company is to bring new affordable and commodity scale products and solutions to market, that extends the frontiers of precision and targeted medicine. renelife.co.in

 

About Aldec

Established in 1984, Aldec is an industry leader in Electronic Design Verification and offers a patented technology suite including: RTL Design, RTL Simulators, Hardware-Assisted Verification, SoC and ASIC Prototyping, Emulation, Embedded Solutions, High Performance Computing, Design Rule Checking, Clock Domain Crossing, VIP Transactors, Requirements Lifecycle Management, DO-254 Functional Verification and Military/Aerospace solutions. www.aldec.com

Aldec is a registered trademark of Aldec, Inc. All other trademarks or registered trademarks are the property of their respective owners.

 

Media Contacts:

Aldec, Inc. 
Christina Toole, Corporate Marketing Manager
+ 1 702 9904400
christinat@aldec.com

 

ReneLife Private Limited
Prof. Debnath Pal, Director
+91 80 23601409
dpal@cds.iisc.ac.in

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