How to merge individual contigs

[kasutubh]

Hi Everyone,

I would really be thankful if anyone is able to tell me solution to the following,

1. I have sequences some BAC clones and have generated contigs. It turns out that 2 BAC's represent same genomic regions..so I would like to merge contigs from both the sources and get larger contigs.
2. Is there any tool whereby I can merge contigs from both the clones?

Thanking you,

[maubp]

Maybe try the classic assembly tool PHRAP? Or do it "by hand" if it really is just 2 BACs's (in a text editor or your scripting language of choice).

[sunyuhui]

I'm having the same problem too...

I've tried Phrap/CAP3/CABOG, but none of them is good enough. Or maybe I missed some important parameters？

Anyone got a good solution？

[maubp]

You could try an assembly editor like gap4 or gap5 for manual finishing.