454 and bacterial genome assembly Q

[amisic]

Hello - Forgive me if this question has been asked many times.

I have 454 bacterial genome sequence data from clinical isolates from which there is a reference genome available. I assembled a genome using the reference with Geneious. However, I'd like to see if I can do better - there were many Ns in this assembly.

What programs do you use and recommend?

Thank you very much for your time and assistance.

[bastianwur]

Is Newbler not the default program for 454 sequences?

[amisic]

Hi - Thank you for your response. I'm working on Installing Newbler now. I've also tried DNAstar's SeqMan Ngen, but have encountered a bug in there (can assemble 454 reads to a reference genome, but can't download the new consensus sequence.

Any other suggestions?