I am trying to find a tool that helps assemble a genome segment from a fastq file, without mapping to a reference genome. I do have the reference genome, but I am checking for diversity between two genomes (specifically indels, MITES etc.) .
As per my understanding, If I assemble the genome denovo and align fasta file, I will lose that information I am looking for as an assembler might filter the repetitive regions.
Any pointers to this will be of great help.