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Importing pre-assembled sequence into Xgap?

Bonfield James jkb at mrc-lmb.cam.ac.uk
Tue Jul 18 04:31:18 EST 1995

Chris Abajian wrote:

>I am told that xgap will now accept pre-assembled sequence.  In
>talking with folks at St.Louis I get the impression that this is
>not yet robust enough to use on a production basis.  Our intent
>would be to use another assembly program to produce contigs and
>then import them into xgap for finishing and to join contigs.

The Sanger Centre use this pre-assemble option in (I think) all their
assemblies now. We are unaware of any bugs in it (but someone please tell us
if we've missed something).

>Is this functionality available?  Can it be done using a recent release
>of xgap?  We have xbap, and considerable hacking is required.  I was

Yes and yes.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 412282
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.

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