FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
How to deal with input trees with no clear rank order or given levels (QIIME includes p, s etc) but a standard CanSNPer tree does not (for example). Should FlexTaxD assume that the top X order follow a certain level structure, or should it require "--skip_rank" or a given file with "translated" ranks? Or should default behaviour be to create a number series for the levels?
How to deal with input trees with no clear rank order or given levels (QIIME includes p, s etc) but a standard CanSNPer tree does not (for example). Should FlexTaxD assume that the top X order follow a certain level structure, or should it require "--skip_rank" or a given file with "translated" ranks? Or should default behaviour be to create a number series for the levels?