What is the difference between meganizing a DAA file, and importing a DAA file
The LCA parameters options are the same. But meganizing a DAA file is much faster.
Meganizing adds classifications and indexing to the end of a DAA file.
Importing a DAA file produces a new RMA file, to which all reads and alignments are copied, so that is way importing takes much longer.
So mechanizing is the preferable option.
The resulting analysis should be the same in either case, although in practice sometimes minor differences occur due to slightly different heuristics are used. For example, when importing, you can set a threshold for the number of alignments to keep, which you can’t do when meganizing.
Also, you can’t use the paired-read option when meganizing.