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Plasmid sequencing is what I’m using it for. Nanopore is the only technology (other than Pacbio) that you can solve the indexing problem with, which MASSIVELY l
by koeng 6y ago
Plasmid sequencing is what I’m using it for. Nanopore is the only technology (other than Pacbio) that you can solve the indexing problem with, which MASSIVELY lowers the cost per sample. Approximately $14 down to $2, which a LOT less manual work (or a lot less robot work)
With plasmids, you can also train custom models to get better alignment results.
It’s insane that nobody else I know of is doing this, since it actually works quite well!
- vikramkr 6y agoAre you sequencing the whole plasmid or just your inserts? The reason I'd never use a nanopore for my plasmid work is because the reason I sequence is to confirm assembly and sequence, especially after cloninf protocols, which is going to be one of the more common (if not most common) use cases for plasmid sequencing. I need Sanger for the base pair level accuracy.
- koeng 6y agoWhole plasmid. In my experience, Sanger is less accurate than Nanopore, especially since you’re getting 1x coverage per read, and in order to reliably get good coverage of sequence you need a primer every 600 base pairs. Consensus reads on Nanopore aren’t that bad, and you can automate them way better than Sanger. I haven’t found any issue using them - IMO the “it isn’t accurate” stuff isn’t very accurate. Also, base pair resolution is bad on Nanopores primarily at homopolyer stretches. Guess what you can’t synthesize in the first place? (Edit: I’ve done Sanger sequencing on about 3,000 plasmids at once before for high throughput cloning, and that SUCKED.)
- Simulacrum_me 6y agoWhat do you mean by the indexing problem in this context?