By Matthew Dublin
BGI has announced the early access release of their newest suite of bioinformatics tools, including some cloud and GPU accelerated applications.
The new release includes an updated version of the Short Oligonucleotide Analysis Package (SOAP), including a GPU-accelerated alignment tool version SOAP3-GPU. According to BGI, SOAP3-GPU performs up to ten times faster than SOAP2 at aligning short reads with a reference sequence.
“To tackle these difficulties, BGI and its collaborators are working on GPU accelerated bioinformatics tools, including alignment and variation detection, for example. The improvements in speed are impressive -- the prototype version alignment tool is ten fold faster than it’s CPU counterpart, while SNP detection codes are about two magnitudes faster,” stated Bingqiang Wang, director of the High Performance Bioinformatics Center of BGI in a press release.
BGI's software package release also includes an upgraded version of Hecate and Gaea, two cloud based distributed solutions that Evan Xiang, director of R&D at BGI's Flexible Computing Center, says will be used to solve research problems in a "flexible" manner — or in other words, researchers can run de novo assembly jobs on the BGI cloud or by downloading the programs and running them on Amazon's EC2 cloud.
While there are no benchmarks available, the BGI announcement claims that Hecate, based on MapReduce, can reduce the cost of de novo assembly by more than 50 percent and Gaea, a SNP calling program, can improve the efficiency of cluster usage by more than 30 percent.