On creating RMA6 files from DIAMOND and other alignment tools

RMA6 is a new version of the the RMA file format used by MEGAN. It contains all reads and matches associated with a sample in a compressed format. These files can be computed directly from a number of different BLAST formats and other types of alignment files, and also directly from a DIAMOND DAA (.daa) file.

MEGAN6 Ultimate Edition comes with a tool called Meganizer
This tool operates on .DAA files produced by DIAMOND.
Meganizer performs taxonomic and functional classification of all reads and alignments in a given Diamond file and indexes all reads by taxonomic and functional bins. The result of this analysis is added to the end of the .DAA file. Such “meganized” diamond files can then be opened in MEGAN6. This process is really fast.
For example, while a DIAMOND alignment of 800 million reads against the full NCBI-nr database takes about 62 hours on a single server, producing over 9 billion alignments, meganization of the resulting .DAA files takes only another 5 hours. So you can perform a full metagenome analysis including taxonomic and functional binning in less than three days on a single server… Standard MEGAN6 functional analysis includes InterPro2GO, eggNOG, SEED and KEGG (if you have a KEGG license)