MEGAN analysis starts with collecting reads from any shotgun platform. Then, the reads are compared with sequence databases using BLAST or similar. Third, MEGAN assigns a taxon ID to processed read results based on NCBI taxonomy which creates a MEGAN file that contains required information for statistical and graphical analysis. Lastly, lowest common ancestor (LCA) algorithm can be run to inspect assignments, to analyze data and to create summaries of data based on different NCBI taxonomy levels. LCA algorithm simply finds the lowest common ancestor of different species.