Length Polymorphism using long read Nanopore

Question

[pixie@bioinfo]

Hi, my lab is working on genotyping plants. A lot of them have very complex ploidies and often do not have a genome. We use old school AFLP. I was wondering if its possible to do a Nanopore sequencing on the PCR amplified fragments. Then we calculate the variations in length to do the genotyping after long read sequencing ? This is just a proof of concept and wondering if its worth a try. Thanks

Answer 1

[colindaven]

Yes, you can do this. I don't know if lengths will be exactly comparable between the two methods.

Some ideas are available in this pipeline - https://github.com/epi2me-labs/wf-amplicon

Note that ONT sequences will be a lot more data rich than just a few lengths (very old school indeed).

[pixie@bioinfo]

thanks, i will give that a read