I have created a scientifically interesting hybrid of two related plant species, but I am not sure if it really is hybrid, so I got low coverage nanopore sequencing for them.
I have relatively good assemblies for both parents. The idea is now to map the reads of the new hybrid to each of the parents, to confirm hybridization.
So far so good, but now if gets confusing: Because the species are related, parts of their genome are similar. Naturally, many Nanopore reads map to both. Furthermore, many reads map to multiple places, complicating the picture.
Total nanopore reads: 516914 Reads mapping to parent1: 632245 | not chimeric: 519048 Reads mapping to parent2: 1122104 | not chimeric: 594088
I have done mapping with minimap2 (with "-x map-ont"), which is very fast, but I'm unsure of how lax it is mapping.
Do you have suggestions on how to continue with the analysis? Strict parameters for minimap? Use other aligner instead? Filter the mapped reads for single hits? An altogether different approach?
When do you think I can conclude that my hybrid really is a hybrid?