I am new in the MEGAN community. I deal with hundreds of metagenomic sequenced samples from nanopore sequencing. I run DIAMOND and meganize with the command line. However, to download all these meganized.daa files to my local Laptop and open them in the GUI takes much time. I wonder whether there is a command line solution to extract biom and newick tree files directly and to download tese files for further analysis in R.
Probably, there are solutions, but I have not found it so far. If so, sorry for this request.
Thank you in advance.