Edico Genome, IBM Collaborate
News May 18, 2016
Edico Genome has announced a collaboration with IBM to make DRAGEN available on the new IBM Power Systems S822LC for high performance computing (HPC). In addition, Edico is now offering the Broad Institute’s Genome Analysis Toolkit (GATK), a software package for analysis of high-throughput sequencing data, deployed on DRAGEN. Called Accelerated GATK, internal testing by Edico suggests that the offering takes only 18 minutes to complete variant calling analysis when run on the IBM Power Systems S822LC for HPC, which in the past has taken approximately 30 hours.
IBM’s Power Systems S822LC’s architecture is ideal for life sciences clients who need more processing power, delivering maximum throughput for applications. The POWER8-based HPC system infuses community innovation from the OpenPOWER Foundation – a 200-member global organization of leading technology suppliers and users supporting and contributing to open development on top of POWER’s open architecture – and will simultaneously increase workload density and reduce data center floor space.
Edico’s DRAGEN and the new Accelerated GATK combined with the Power Systems S822LC help enable users to benefit from performance that has the potential to allow advanced analytics to be performed using the integrated platform, potentially reducing the need for multiple bioinformaticians or a supercomputer-class compute infrastructure.
“As more leading medical centers, clinical labs and research institutions work on genomic medicine, rapid and accurate analysis of next-generation sequencing data is critical,” said Sumit Gupta, vice president, high-performance computing and analytics, IBM Power Systems. “The IBM Power Systems S822LC for high performance computing, combined with Edico’s DRAGEN Bio-IT processor, accelerates genomic sequence analysis from hours to minutes, enabling scientists and doctors to speed up their genomic research.”
“IBM is one of the leading providers of informatics infrastructure to hospitals around the world, with the majority of hospitals in the U.S. utilizing their technology solutions,” said Pieter van Rooyen, Ph.D., chief executive officer of Edico Genome. “Providing DRAGEN on IBM Power Systems offers both existing IBM customers and additional hospitals and academic centers seeking to build a genomics infrastructure with a rapid, accurate and easily integrated analysis solution. In addition, our new offering, Accelerated GATK, enables genomic researchers to access a comprehensive toolkit of algorithms in one spot, further streamlining their biomedical research activities.”
As part of the collaboration with IBM, Edico Genome has joined the OpenPOWER foundation. This will enable Edico Genome to access POWER CPU processors and systems platforms for optimization, development activities and advanced hardware technology exploitation. GATK is a software package developed at the Broad Institute to analyze high-throughput genomic sequencing data. To date, more than 20,000 users have processed genomic data using GATK, which offers a wide variety of genomic analysis tools.
DRAGEN is highly reconfigurable, using a field-programmable gate array (FPGA) to provide hardware-accelerated implementations of genome pipeline algorithms, including BCL conversion, compression, mapping, alignment, sorting, duplicate marking and haplotype variant calling. In addition to Accelerated GATK, pipelines available on the DRAGEN platform include Transcriptome/RNAseq, Metagenome/Microbiome, Epigenome/Methylome and Joint Genotyping.
All of the pipeline algorithms can be run on IBM Power Systems and updated versions are made available for customers through simple remote downloads. The Genome Pipeline can be used for analysis of both human and non-human genomes, including wheat, rice, mice, rat and other genomes. The flexible DRAGEN platform allows for custom algorithm development as well as refinement and improvement of existing pipelines.