otutable limited to taxonomy level 3

[marcadella]

Any reason why otutable limits the taxonomy level to 3?

[jfmrod]

Hi, its missing from the command help page, but you can choose the level and which taxonomy you want the OTU table to be generated by using the arguments -tl and -ti. The level 3 is 97% OTUs which is one of the common species level choices, but you can choose 4 or 5 for higher OTU resolution or 2 or 1 for lower (more broad) OTU groups.

You can also get the NCBI taxonomy count tables using -ti 1 instead of the default -ti 0 .