With the latest release, 6.19.0, MEGAN now offers two taxonomic classifications of reads: the default remains based on the NCBI taxonomy, but, in addition, MEGAN also performs taxonomic binning of reads using the GTDB taxonomy, using the same algorithmic parameters as set for the NCBI taxonomic analysis.
That is great news!. Should I use new mapping files and the files for this?.
I also have been trying to download the new version of MEGAN but it seems that the website is not working currently. Should I wait a few more days and try it again?
Yes, please use the May 2020 mapping db file if you want to compute the GTDB-based taxonomic analysis as well.
The server should be back up now (it was down due to air-con failure in the server room and might go down again for air-con repairs…)