For a project I'm trying to find out which aligner is best for aligning whole bacterial genomes.
Important aspects for choosing the best aligner are speed and sensitivity. In this situation NUCmer and BLAST seem both great programs for making the local alignments. To find out which suits best, I've ran some tests. I found out that
- MegaBLAST is a bit more sensitive than NUCmer, because it finds more alignments, but also breaks off alignments more quickly.
- At the aspect of speed NUCmer is BLASTed away with a factor of 3 to 4. Both programs are very fast though.
My question remains, what advantages would one have when using NUCmer instead of BLAST?