Taxonomic read counts

Hi MEGAN Community!

I am new in MEGAN, and I am interesting in a particular feature of this tool: Taxonomic profiling

For the purposes of my work, it is essential to obtain an estimate of the abundance of microorganism associated to the samples, at the species level.

I read the MEGAN paper and it is not clear to me if I can do this whit this tool. An ideal output for count reads will be:

B. subtillis 35 counts
P. fluorecens 50 counts


Can I have something similar with MEGAN?

Thank you for your help!

By definition MEGAN is a binning tool, i.e., it does not do any approximations for the content of the sample.

MEGAN treats each read independently and finds the best place for it on the taxonomic tree based on its alignment to the database (most commonly NR). Therefore, if it comes from the conserved region of the bacterial genome, it could be placed in the higher taxonomic ranks. However, you can minimize that with parameters.

You can export the tax to count table, so format-wise it is not a problem.