Easy to use local assembly programs ?

Question

[Zev.Kronenberg]

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.

Answer 1

[Erik Garrison]

Look no further than Scalpel.

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

Answer 2

[Zev.Kronenberg]

The latest version of Abyss can take a paired-end BAM file as input.