I want to improve the identification of the microbial communities from several metagenomes that I recently sequence, by using different databases in MALT alignment. I built the index for malt using the GTDB reference database (24,706 species clusters) and then align my data against this index (obtaining .blastn.gz files). However I have a couple of questions regarding the visualisation of these results using Megan:
- How could I get a mapping file to use blast2rma after malt alignment?
- How could I create the .tre and .map file of this database to use it in MEGAN?. GTDB provides a .tree for bacteria and a separate .tre file for archaea (Newick format). I am not sure about how to concatenate both to use it together or if it is even possible to do this. I don’t find any .map file available.
Thank you very much!!