The main feature of this new version is the possibility to filter a bunch of contaminants (danio,human,mouse,mosquito,phi) with the option -c.
masque -c mouse,human,phi -i ... -o...
I recommend to filter the host and the phi phage only.
Plus, several databases have been updated: SILVA (16S/18S/23S/28S) and unite, underhill for ITS.
Masque also include an improved phylogenetic analysis of OTU sequence by using more accuratly mafft, BMGE to select portion of OTU with most informative data and IQ-tree (with option --accurateTree) to perform the tree.