NEW YORK (GenomeWeb) – Bioinformatics startup Genalice said this week that its flagship read alignment and variant calling tool has been selected as the primary next-generation sequencing data-processing technology by plant genomics firm KeyGene.
Since the companies first partnered in 2012, Genalice has forged a number of additional deals with ag-bio players, Chief Business Officer Jos Lunenberg told GenomeWeb this week, reflecting its efforts to optimize the technology — called Genalice Map — for plant genomics applications.
Although Map has mainly been used as a tool for human genomic research, in 2012 Genalice licensed the platform to KeyGene, which was having difficulty handling the increasing amount of data it was generating for its customers, Lunenberg said.
At that stage, Map was still a first-generation technology and it wasn't entirely clear how well it would perform in plant genomics.
"Those are very difficult data to align and call because there are a lot of repetitive areas," he explained. Further, many plant species are polyploids, which adds another layer of complexity. "It's a different ball game" than with human genomes, Lunenberg said.
Rather than tweak algorithms designed for human genomics, Genalice "started from scratch," creating algorithms for Map that take into account the variability between human and plant genomes, Lunenberg said.
"The human genome has 3.2 billion base pairs," he noted. "We know plants that are 5 million, 10 million, 20 million, and most algorithms simply cannot handle these large genomes. We made sure we could."
That effort included working with KeyGene to validate Map in various plants, including two tomato species.
"We first went through the validations for alignment and variant calling on smaller plant genomes," Roeland van Ham, vice president of bioinformatics and modeling at KeyGene, said in a statement. "Thereafter, we covered the adaptation of … Map to also process larger plant genome sizes."
Based on the outcome of that work, KeyGene is now using Map as its main data-analysis tool in all of its high-volume NGS projects, van Ham added.
Meanwhile, Lunenberg said that Genalice has been steadily adding new features to Map as the NGS field continues to evolve.
Matching trends in the human genomics space, population-based calling and RNA-seq alignment and quantification are becoming increasingly important to those working in plant genomics, he noted. As such, Genalice is putting the finishing touches on these functions within Map and expects to introduce them in the coming months.
Since its foray into ag-bio through the KeyGene alliance, Genalice has signed on a number of additional partners in the area, including five undisclosed companies that Lunenberg said are in the final stages of validating the technology in their own labs.
In the next few months, Genalice anticipates that at least two of these firms will select Map as their main data-analysis technology similar to KeyGene.