I don't know what all the fuss is about. If molecular biologists simply learnt some basic Unix command line tools, they could rid themselves of messy PCRs, oligo design, optical maps, primer walking etc.
% echo ">ClosedGenome" > closed.fasta
% grep -v '>' 454AllContigs.fna | sed 's/[^AGTC]//gi' >> closed.fasta
% mail -s "Genbank genome submission" email@example.com < closed.fasta
Too easy! :-P