4 ms·
Should the long read lengths allow error correction to work well if there is sufficient coverage?
by anon946 6y ago
Should the long read lengths allow error correction to work well if there is sufficient coverage?
- fwip 6y agoNanopore/pyrosequencing technology is interesting in that the class of errors that it is most susceptible to (homopolymer inaccuracies) nearly do not exist in more traditional base-by-base sequencing. These have proven harder to correct than simple substitution errors - this is both a fault of the bias of existing tooling, and also a difficult problem in general. Roche and other companies have had a lot of smart people working on this problem. Increasing coverage will definitely help resolve these errors, but the coverage required may be such that it's more cost effective to use a more traditional sequencer. A homopolymer is when you have stretches of the same nucleotide, and the error is miscounting the number of them. e.g: GAAAC could be called as "GAAC" or "GAAAAC" or even "GAAAAAAAC".
- dnautics 6y agoWhat? Have you ever looked at a sanger trace with homopolymer stretches? Depending on how blotchy it is, After about 7 you might not really be sure, and it definitely gets the n wrong occasionally even with nicely resolved peaks. I'm not defending nanopores here, frankly I'm not convinced about them yet.
- fwip 6y agoSorry, I didn't mean Sanger sequencing, was comparing to Illumina sequencing.
- jakobnissen 6y agoOnly somewhat, because the errors are systematic, and not random. Using the R9 pore flowcells, I've basically given up on getting correct consensus sequences even for influenza genomes (without manual correction, which is too labour intensive). Perhaps the new R10 pore, much better at homopolymers, will solve the problem.