Next Generation Sequencing



At Lawrence Livermore, a first-of-its-kind supercomputer with expanded dynamic random access memory (DRAM) and persistent non-volatile memory (NVRAM) is being used to solve big data problems in areas such as business analytics and bioinformatics. In fact, bioinformatics scientist Jonathan Allen is using the new technology for a next-generation sequencing technique known as metagenomic sequencing. In his field, Allen is working on new methods to rapidly detect and characterize pathogenic organisms, such as viruses and bacteria, in a biological sample.

To that end, Allen’s team is developing scalable analysis tools that can be used to compare short genetic fragments in a query dataset to a large searchable index of genomes. With the resulting information, he can make determinations about the potential threat an organism poses to human health. Traditional technologies make it difficult to rapidly search a database of reference genomes, but with the unique capabilities of Livermore’s supercomputer, Allen and his team are able to store large reference databases of genomes and execute expansive analyses with higher resolution. The technology allows his team to process hundreds of samples in a short amount of time—a marked improvement over the much slower speed and smaller storage capacity of a traditional desktop.

You can read more about Livermore’s supercomputer here.