Why don't my de novo assembled contigs not have continuous ensembl blat alignments with a closely related reference genome? For example, I have a certain stretch of my contig with 100% identity, and then a new alignment begins after 10 bases (of the subject), and I get a score of say 99% and then another one with 97% identity. These hits point to the same locus of the reference. How can I have the entire stretch represented in one alignment, with gaps inserted if required, even if the identity goes down? That would help me in comparing the entire contig at once with the reference.
QUAST is a tool designed to do what you want. It does so using local alignment, though - which, in my view, is the appropriate approach to the problem.
If you are so adamant on using global alignment, you may try your luck with LAST with the
-T 1 parameter:
Type of alignment: 0 means "local alignment" and 1 means "overlap alignment". Local alignments can end anywhere in the middle or at the ends of the sequences. Overlap alignments must extend to the left until they hit the end of a sequence (either query or reference), and to the right until they hit the end of a sequence.
Warning: it's often a bad idea to use -T1. This setting does not change the maximum score drop allowed inside alignments, so if an alignment cannot be extended to the end of a sequence without exceeding this drop, it will be discarded.