(To be expanded)

1. Build and install MIRA and documentation according to the INSTALL file (or
   grab a binary distribution)
2. Read the "MIRA USAGE" introduction. The html version can be found in the
   doc/docs/html directory
3. Read the main MIRA introduction
4. For 454, Solexa, Ion Torrent assembly, read the corresponding chapters in
   the documentation.
5. Copy the minidemo directory to a temporary location (e.g. "cp -r minidemo
   /tmp/miraminidemo") and play around with the demos provided there.

For viewing/editing assemblies, an assembly editor is recommended. Have a look
at GAP4 (from the Staden package, see
http://www.sourceforge.net/projects/staden/), MIRA generates output suited for
import into gap4 (by using caf2gap)

James Bonfield released a working version of gap5. Import into gap5 is done
with CAF files and the "tg_index" tool supplied in the gap5 package.

 
Other people use consed, but I don't know whether it's able to cope with the
amount of data present in Solexa projects.
