Just wanted to say "Hello" to everyone, and glad to see this wonderful site up and running as I will probably have many questions in the near future. I'm a post doctorate researcher, and have some experience with 454 sequencing of bacterial genomes. However, the genomes that I have experience were fairly small (~1.8 Mb) compared to the genomes that I'm now working with (~5.5 Mb), in addition the new genomes have lots of bacteriophage and inverted repeats. The genomes have been assembled [I]de novo[I] using paired end and whole shotgun sequencing, however there are still over 200 contigs per genome. I'm in the process of filling the gaps using PCR and Sanger sequencing, however any suggestions that people have about ways to assemble would be much appreciated. 