MEGAN and annotation requirement questions

I am looking into using MEGAN for metagenomic analysis. I have several metagenomes I need to compare for both taxonomy and function. This data has already been sequenced, assembled, and annotated by JGI using their standard pipeline. I would prefer against having to annotate the FASTA files myself, but essentially none of the annotation done by the JGI has been done by blast, but instead HMMER. Is there any compatibility for using this data with MEGAN6? I have access with gff files along with a bunch of tsv files that have varying amounts of information in the file and I can trim things as needed from them. Are there any suggestions for what would be the best method for inputting this annotation into MEGAN, or would I be better off using BLAST myself?

Hi Alex, I wrote a HMMR parser a long time ago. It’s not currently part of the MEGAN package. If you sent me a small example file, then I will look into whether I can get it to work on your data