The 3.9 line of MIRA is the development line of MIRA which will ultimately
lead to MIRA 4. It's the result of 10 months of work since the last 3.4.x
versions and much has changed. A lot behind the scenes, but also interesting
things for everyone, most notably in speed and quality terms. The most
important changes for users: the interface. Please absolutely do consult the
section on manifest files in the documentation!
Users with Ion Torrent, PacBio or Illumina (especially RNASeq) data should
prefer these versions over the 3.4.x line.