This command re-orders (and possibly reverse-complement) the strings in the collection to minimize the number of runs in the abundances and, hence, optimize the encoding of the abundances. This is achieved via the program ./permute which, in turn, uses the builder/cover.hpp class to build the permutation.
This command re-orders (and possibly reverse-complement) the strings in the collection to minimize the number of runs in the abundances and, hence, optimize the encoding of the abundances. This is achieved via the program
./permutewhich, in turn, uses thebuilder/cover.hppclass to build the permutation.