1. Software packages for next gen sequence analysis: SEQanswershttp://seqanswers.com/forums/showthread.php?t=43
2. Software/list SEQwikihttp://seqanswers.com/wiki/Software/list
3. Sequence Assemblyhttp://en.wikipedia.org/wiki/Sequence_assembly#Available_assemblers
4. CAP3: A DNA Sequence Assembly Program
5. Phred, Phrap, and Consed (Green Group)http://phrap.org/phredphrapconsed.html