Chris Abajian <chrisa at bozeman.mbt.washington.edu> writes:
> 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 Center has been making use of the "preassembled" feature
since early this year. It is now very robust, though it is a little
tricky to get your data in the correct format. We assemble using the
PHRAP program written by Phil Green, then do our editing within gap.
The marriage works well.
Our approach is to represent assembly information using a textual
interchange format. We have tools to read assemblies into GAP and also
ACEMBLY (Jean Thierry-Mieg), and extract assemblies from GAP and PHRAP.
Having an independent representation also means we can do a lot of our
own post-assembly processing before letting the user see the data.
If anyone is interested in getting our tools, please email me.
Simon Dear sd at sanger.ac.uk