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?

Thank you!

This means at most one alignment per reference per read is reported.
In other words, if a read R has more than only alignment to a given reference X, then only one alignment between R and X is reported. Alignments of R to other references are still reported, and likewise, alignments of other reads to X are still reported.