Is directly using DIAMOND to assign taxonomy for reads not recommended? #138
Description
Hello team,
Thank you for providing the RAT tool. It has saved me a lot of time by efficiently combining information from MAGs and contigs to annotated taxonomy for reads.
I noticed that the file named *.complete.abundance.txt marks the "unmapped" reads as a single lineage labeled "unmapped," without providing further details.
If I want to retrieve the detailed lineage for the unmapped reads, it seems I need to parse the *.read2classification.txt file myself.
May I ask about the rationale behind this design choice? Is annotating taxonomy for reads directly with DIAMOND not recommended, or is there another reason?
