As title, and the following is the background FYI :
I am discovering a possible single copy insertional mutation in a nonaploid plant genome.
Previously I used SPades to assemble contigs of the mutant using reads containing the potentially mutated sequence, which then has given me a ~1000 contigs of the mutant genome.
While ~10 contigs containing breakpoints seems to have been discovered after mapping of reads (0 mismatch) to the set of 1000 contigs, after PCR screening, they all are false-positive.
Then I redo the mapping again using default no. of mismatch set by bwa, discovering reads with mismatches corresponding to the breakpoints actually joined the breakpoint and resulted in no difference between the wild-type and the mutant mapping result.
After that, I started to consider if the assembler "generalize" my contigs too much that makes the breakpoint difficult to be discovered by observing the difference between the wild-type and the mutant.
That comes to my question: is there any contig assemblers which respect a single copy mutation in a nonaploid genome? The situation is discovering the 1 in the 1:8 situation in the genome.