On-the-spot genome analysis
The ability to read the genome – all the DNA of an organism – has vast potential to understand human health and disease.
Researchers at the Garvan Institute of Medical Research and UNSW Sydney have published a method to take genome analysis ‘offline’, by adapting a computer algorithm that can perform accurate analysis – with far less computer memory than current programs. The scientists’ algorithm may make it possible to identify infectious diseases in remote locations, or at the hospital bedside, using the computational memory of devices as small as a smartphone.
“Other algorithms, which take a similar approach of splitting up the reference data, produce a lot of spurious and duplicate mappings – just like overlapping photos in the panorama. What we did in this study was fine-tune parameters and select the best mappings across several small indexes. This approach gave us similar accuracy as current standard genomic analyses, which previously required the memory available in high performance computers,” says Dr Smith.
Research article: Featherweight long read alignment using partitioned reference indexes