I am trying to search for the point of insertion (possibly transposable element) between a wild-type and a mutant plant genome (estimated size 7500Mb) from illumina 150bp pair-end short reads. Sequencing depths of the wild-type and mutant genome are around 38 and 11. A k-mer comparison approach was used to pinpoint the mutation (generally the same principle as described here : https://www.nature.com/nbt/journal/v31/n4/full/nbt.2515.html)
I have some miscellaneous questions which I want to seek advice for :
1) Are the sequencing depths of 38 and 11 too low?
2) If more depth is required, do you think long-reads (e.g. oxford nanopore) has a better cost performance than short-reads, provided I have some short reads data on hand already?
3) Any recommendation on the assembler which works well in reconstructing the junction between non-repetitive (i.e. wild-type region) and the repetitive region (e.g. transposable element)?
Any other teaching would be much appreciated.