DNAStar this month will release a new version of its flagship Lasergene sequence-analysis software with a new algorithm for assembling reads from 454 Life Sciences’ Genome Sequencer 20.
The new release, Lasergene 7.1, will include an updated version of the company’s SeqMan contig assembler called SeqMan Pro. The new algorithm is able to handle more — and shorter — reads than previous versions of the assembler, according to Jeff Engelking, technical sales consultant at DNAStar.
“Our classic contig assembly algorithm was able to handle along the lines of 10,000, possibly 20,000 sequences in a given assembly,” Engelking said. “And in this new algorithm, on a desktop computer, we’ve increased that capacity by about 100-fold. We’re now able to handle some million or more reads that are required for adequate coverage of a viral or bacterial genome.”
Tom Schwei, vice president and general manager of DNAStar, said that the new software is also able to handle the assembly challenges that arise from 454’s relatively short read lengths.
The software has been “optimized” for the approximately 100-base-pair reads of the 454 system, but shorter reads from other next-generation sequencing platforms, such as Solexa’s and ABI’s upcoming system, still represent a challenge.
Those systems, which generate reads in the neighborhood of 20 bases, present “some statistical issues,” Engelking said. “There are only four bases in DNA and when things are that short, putting together that puzzle, you can have a lot of false joins.”
SeqMan Pro is applicable to either de novo assembly or assemblies that use a reference genome as a backbone, Engelking said.
In de novo assembly, the algorithm generates contigs that are “on par” with 454’s assembler in terms of contig length, he said. The two algorithms actually generate different contigs, he noted, which means that the two packages could be used together to produce more accurate genomic assemblies.
“The key for us, of course, is to keep up with these technologies to make sure that when the sequencing machines are out there delivering data, that there are tools out there ready to handle it.”
“We don’t really view this as we’re trying to replace the 454 assembler or be in competition with them,” said Schwei. “This is where our area of expertise as a company has been for more than 20 years, [and] we’ve had discussions with 454 and they don’t view this as necessarily one of their areas of core expertise. They’re happy to have other organizations who have strength in this area, like DNAStar, work on the assembly engine and the analysis software beyond what their basic engine is able to accomplish for customers.”
DNAStar was founded in the early ‘80s and has seen its share of ups and downs in the bioinformatics market. Schwei noted that recent developments in the next-generation sequencing sector — alongside high-profile initiatives like the recently launched X Prize for Genomics and the National Human Genome Research Institute’s $1,000 Genome initiative — have brought “a level of enthusiasm and excitement to the market … that hasn’t been there for many years.”
But even as the company is “excited by the resurgence of interest in this area,” Schwei noted that “the key for us, of course, is to keep up with these technologies to make sure that when the sequencing machines are out there delivering data, that there are tools out there ready to handle it.”