Discard too short reads
Reads that are too short (e.g. < 60 bp) will generate false positive alignments and introduce bias downstream (gene counts, mgs abundance etc.) fastp and trimmomatic are very permissive regarding minimal read length after quality control (15 and 36 bp) with default parameters (that most users will use). Thus, just like mOTUs or MetaPhlan, Meteor should reject too short reads (before or after alignment?).