Given that the recommended load amount for rapid PCR barcoding is 1-5 ng, and there is previous ONT research that a 10% flow cell load can still be useful for sequencing, I'd say 0.1 ng.
Of course, it always depends on the application. Sure, you can go low, but you're not going to get good yield.
In that case a PCR-based kit should be fine. Genomes that small are usually sufficiently non-repetitive that the shorter reads from PCR amplification (~2kb) aren't a problem for assembly.
Oooh. Perfect. Thank you! This would be for a culture/very low diversity enrichment and we can get/already have illumina. So should turn out pretty well.
No experience with that specific type of sample unfortunately. No yields from say direct filtering to a small 0.1um filter & PowerSoil extraction? Maybe @jenskallmeyer.bsky.social has seen similar low biomass samples?
Comments
Of course, it always depends on the application. Sure, you can go low, but you're not going to get good yield.
In that case a PCR-based kit should be fine. Genomes that small are usually sufficiently non-repetitive that the shorter reads from PCR amplification (~2kb) aren't a problem for assembly.
We didn't have great nanopore results with low amount of material, the PCR approach may help but just process more biomass if possible.
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-023-09853-w