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by alwaysdoit 1962 days ago
If you repeat the process many times will it reduce that error rate, or are the errors non-independent?
2 comments

Unfortunately, with nanopore the errors are biased so you tend to get errors in the same places. All sequencing techniques also have error rates but some are unbiased so running a single sample through (which will usually have many, many copies of any sequence) will average out to a good read of the sequence.

Some good info on next-gen sequencing techniques: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841808/

Still, some of the errors can be compensated for with more coverage. So if you can manage 20-30X you're left with the homopolymer problem (nanopores can't tell how long a stretch of the same repeated nucleotide is, because you can't control how long the sensed kmer stays in the pore), but lots of other types can be improved quite a lot.
Last time I looked into Nanopore the cost wasn't that much better where you'd even consider this experiment.

On the other hand, when doing a genome assembly, the Nanopore reads are good for a draft sequence and then the Illumina reads can be used to polish the sequence.