Greetings,

I'm trying to get a sense of what people are using for local assembly. Ideally I'm looking for a tool that takes a BAM file and outputs a fasta for a region of interest.

EDIT:

I'm working with whole genome data.
Look no further than [Scalpel][1].

I've hacked out [the microassembler component of scalpel][2]. It does basically what you're describing except it produces an assembly graph from the BAM file in a particular region.

 [1]: http://scalpel.sourceforge.net/
 [2]: https://github.com/ekg/microassembler