Hello,
I have the same issue as MEGAN Assignation after MALT. I want to create a viral only RefSeq database for MALT, but get classifications outside of viruses.
The alignment is correct, but not the classification. For example classifying a sequence which is part of ‘Human papillomoavirus type 5’ is aligning to ‘Colobus guereza papillomavirus type 2’ which is fine, but the classification reports the primate ‘Colobus guereza’. So clearly the alignment is correct, but not the taxonomy.
For the taxonomy I have tried the following two files, resulting in the same problem:
megan-nucl-Jan2021.db (from MEGAN website)
nucl_wgs.accession2taxid.gz (from NCBI)
Which taxonomy file or which parameters should I use to get an appropriate classification? Thank you for your advice.