For ref mapping you may try TMAP https://github.com/iontorrent/TMAP

I've heard of people having decent success with MIRA, although I haven't tried it myself http://www.chevreux.org/projects_mira.html

Thanks for the response. I looked into MIRA, but my problem with MIRA is here

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#chap_iontor where, Chevreux gives this warning...

"Ion Torrent is pretty new and I did not have as much data to analyse as I had with Sanger, 454 or Solexa. MIRA has been configured to automatically work well with data currently available on the market and with data which is to be expected during the course of 2011 / 2012."

MIRA3 directions are somewhat confusing on that page and it seems they are still for denovo assembly, but I know there has to be a way to use a reference genome.

Also I'm not doing full genomes. I'm only sequencing about 48 amplicons at a time. I'm not sure if this makes a difference as to which assembler I use, but it is something to consider.

I wasn't sure if people were using Newbler, or DNASTAR......