Dear MEGAN community:
Regarding MALT, I’m a bit confused as to what this command does:
“Maximum number of (non-overlapping) alignments per reference. Default value: 1. MALT reports up to this many best scoring matches for each hit reference sequence.”
My interpretation is that the default setting of 1 only allows 1 alignment per reference? e.g. I have 3 reads that align to a specific location on a genome, with the default setting, only 1 of these reads are retained in the alignment?