We have assembled several contigs from SOLEXA reads, now we try to mapped these contigs onto a related reference genome. we used blat to do this work, the problem is that blat hits distributed broadly along the chromosomes, although blat can link these hits into larger blocks when we used PSL output format, but the link made by blat were poor. for example, the contig is only 10kb in length, but when mapped to reference, then link by blat default settings, it span for more than 500kb.
beside blat, are there better mapping tools?
we also tried mummer, but the problem for mummer is that it did not link segments of hits, thus the result is hard to be used.