Alignment delta options
For multiple switches, order of operations is as follows: -i -l -u -q -r -g -m -1 -b.
If an alignment is excluded by a preceding operation, it will be ignored by the succeeding operations. An important distinction between the -g option and the -1 and -m options is that -g requires the alignments to be mutually consistent in their order, while alignment delta options -1 and -m options are not required to be mutually consistent and therefore tolerate translocations, inversions, etc.
In general cases, the -m option is the best choice, however -1 can be handy for applications such as SNP finding which require a 1-to-1 mapping.
Finally, for mapping query contigs, or sequencing reads, to a reference genome, use -q. The duplications printed with the -b option are -r and -q alignments that are not present in the 1-to-1 alignment. These alignments are also the difference between the -1 and -m alignments SEE ALSO The -b option originates from mugsy that provides a code copy of mummer with additional patches. Ubuntu and Canonical are registered trademarks of Canonical Ltd.