While the Illumina platform is the most widely used technology in whole genome sequencing (WGS), an emerging technology shows exciting promise. Because the Oxford Nanopore technology produces very long reads, it is possible to ?close? genomes, identifying chromosomes from plasmids. Combining bioinformatics tools to close the genome with tools to identify alleles contributing to AR conditions, it will be possible to develop a bioinformatics pipeline to determine the location of the alleles within a genome. WA PHL plans to develop these tools along with a laboratory protocol for routine use of the MinION in AR analyses, and validate these paths for clinical reporting. WAPHL holds several key elements making this project feasible, including two microbiologists already trained in the technology, a resident bioinformaticist, an AWS account as an environment to develop analysis tools, and several microbiologists already trained in the concepts of WGS.
While the Illumina platform is the most widely used technology in whole genome sequencing (WGS), an emerging technology shows exciting promise. Because the Oxford Nanopore technology produces very long reads, it is possible to ?close? genomes, identifying chromosomes from plasmids. Combining bioinformatics tools to close the genome with tools to identify alleles contributing to AR conditions, it will be possible to develop a bioinformatics pipeline to determine the location of the alleles within a genome. WA PHL plans to develop these tools along with a laboratory protocol for routine use of the MinION in AR analyses, and validate these paths for clinical reporting. WAPHL holds several key elements making this project feasible, including two microbiologists already trained in the technology, a resident bioinformaticist, an AWS account as an environment to develop analysis tools, and several microbiologists already trained in the concepts of WGS.
