Please circumstantiates your topic. I mean, what is the specific issue in which you deal with?
Duplications in the genome. The intrinsic complexity of the genome. If you get a repeated segment from your sequencing, where you are going to place it in your assembly. That is hard.
Of course, repeats can be exact and inexact. Will the minor differences in your raw sequence matter? It may be simply sequencing errors.
I guess if you have very long reads, with many unique regions that can anchor it in the genome, then the assembly task is not that hard. That said, where are you going to get the extremely long, unfragmented sequences. I guess PacBio is one option, Oxford Nanopore is the other. Oxford Nanopore reads are not good quality reads, so it may be hard to use for now. Long term, I hope Oxford Nanopore can provide high-quality reads. If the read length is over 10K, then assembly of genome is trivial. I repeat, it is trivial!
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