I'm doing genome assembly using SOAPdenovo2-MUMmer3 pipeline. After scaffolds were built, I used
nucmer to align each scaffold to chromosome based on the reference genome.
nucmer alignment, Scaffold18596 is located in chr.5 (only 530 bp match chr.5 but it's the highest score). However, if I simply
blat the sequence of Scaffold18596 to the same reference genome, I found there're several perfect matches in chr.1 (11,360 bp, 3,618 bp, 2,445 bp).
In this case, why
nucmer gave me this strange result? For the command, I just simply used
nucmer -p <Reference> <Query>