Nucleotide mapping and analysis using MEGAN


Is there a tutorial available for mapping reads/contigs against a nucleotide database and then processing this output with MEGAN? I guess this is also similar to using BLAST, but I also cant find a simple tutorial for this!

I can see some guidance online for this from various sources, such as this paper ( but I would like to make my own solution and understand what is going on behind the scenes.

I understand the main points of the workflow, but I am finding, for example, that MEGAN is not working because the sam file is not reporting the mappings with the correct NCBI taxonomy.

Are you able to point me in the direction of some further help?

Megan looks extremely promising, but the application this is needed for requires the analysis to be done quickly, so DIAMOND/LAST appear to be too slow.


If you want to use minimap, then this preprint provides some info on how to perform such an analysis: