Hi, is anybody using, or has tried, Oxford Nanopore MinION for pathogen analysis and identification, microbial metagenomic and similar tasks?
I knew that it wasn't very precise and gave a read accuracy around 90%.
Which are your impression? Is it fine for simple (and fast) sequencing and identification, or for viral or bacterial genotype discrimination?
Thanks
That accuracy is a bit out of date (it's now "around" 90-95%), and bear in mind that it's single-base accuracy. The long-read advantage (in some cases over 100kb) means that matches based on a single nanopore read can be more precise than thousands of short reads.
Nanopore works for identifying metagenomic content, mapping full-length cDNA (or RNA) isoforms, analysing large-scale structural variation, and assembling sequences into assembly scaffolds.
However, if you want the precise sequence of an organism (especially if you only want to use a single read), a hybrid approach is currently necessary. There is still a little bit of lingering systematic error in the nanopore base-calling (not the raw signal) which means that even consensus sequences at infinite coverage are not 100% accurate.
That accuracy is a bit out of date (it's now "around" 90-95%), and bear in mind that it's single-base accuracy. The long-read advantage (in some cases over 100kb) means that matches based on a single nanopore read can be more precise than thousands of short reads.
Nanopore works for identifying metagenomic content, mapping full-length cDNA (or RNA) isoforms, analysing large-scale structural variation, and assembling sequences into assembly scaffolds.
However, if you want the precise sequence of an organism (especially if you only want to use a single read), a hybrid approach is currently necessary. There is still a little bit of lingering systematic error in the nanopore base-calling (not the raw signal) which means that even consensus sequences at infinite coverage are not 100% accurate.
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