Software - MIRA
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina) and PacBio data. It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently - and especially accurately
Support site:
http://sourceforge.net/apps/mediawiki/mira-assembler/
http://sourceforge.net/apps/mediawiki/mira-assembler/
Freeware