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0 pointsampdepolymerase4y ago0 comments

I recommend reading this review

https://genomebiology.biomedcentral.com/articles/10.1186/s13...

I guess there are limits to ensemble methods if the underlying accuracy doesn't increase. I don't work on gene sequencing algorithms but from what I understand of ML ensemble techniques, there are certain assumptions regarding the underlying independence of the errors. The errors for nanopore should be uniform but I am not sure. Any molecular biologist here care to comment?

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biophysboy4y ago

I know that the error rate of the oxford nanopore sequencer depends on GC content (guanine/cytosine nucleotides), and that the Pacific Biosciences sequencer uses a polymerase that gets worn down during reading. So there is some non-uniformity in the chemistry.

ampdepolymeraseOP4y ago

GC rich regions as in hairpin loops? How would the sequencer deal with those?

biophysboy4y ago

If I'm not mistaken the nanopore tech unwinds double-stranded DNA during the reading, so I don't think hairpins are the issue.

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biophysboy4y ago

ampdepolymeraseOP4y ago

GC rich regions as in hairpin loops? How would the sequencer deal with those?

biophysboy4y ago

If I'm not mistaken the nanopore tech unwinds double-stranded DNA during the reading, so I don't think hairpins are the issue.

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