I have a whole genome paired ends sequencing data, divided into R1 and R2. I do not have the reference for the organism I am working on (only a close related one), and I am trying to manually assemble a part of the genome, the centromere, using the paired ends reads I have. I know the starting point and starting from a certain read, I want to elongate it in order to assemble that portion. Could you give me advices for this operation? I could take a part of the read and using grep command search it in the whole genome data, but I am not sure this is a way. Automatic assemblers such as Spades don't work because my genome is a large eukaryotic genome. Thank you!