Fosmid Assembly Recommendations

[Brett Bowman]

I'm putting together a pipeline for the automated assembly of Fosmid sequences, and I'm looking for recommendations of which tools to use.

I've got sets of 5-10 HQ fosmid assemblies, approximately ~QV30/99.9% and 40kb in length, that I want to assemble into the sequence of the original BACs from which they are derived. Problem is, given the fosmids size and repetitve content getting that last assembly step consistently is hard.

Tried so far:
Minimus - Works decently, but has a couple of problems. Appears to sometimes trim the ends of my contigs. Some times misses junctions or creates miss-assemblies.

Celera Assembler - Won't even start, as the 40kb fosmids are apparently too large

Suggestions?

[dgscofield]

For fosmids I've had success with Phrap. Vector sequences left over in your fosmid reads can cause misassemblies so clean them (could be difficult) or add the vector to vectors.seq in Phrap to deal with them. Phrap seems to sometimes be a bit too greedy but I havent' done much tuning to date. It has no problem with fosmid-size sequences. Used in concert with cross_match to map your reads back, and consed to view everything, it can be a very powerful package to check and edit your assemblies.

Cap3 is another assembler that could probably do the trick but I haven't used it yet.