James Bonfield - 2004-08-17

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It is possible to assemble a large text sequence into a gap4
database in the same manner that you assemble other
sequences. If you put this at the start of your file of
filenames then it will be assembled first (assuming you do
not use one of the external assembly tools, such as phrap,
cap or fakii). A sequence does not need to be labelled as
"reference sequence" for it to be assembled and compared

The only thing that this doesn't do is to force all traces
to be compared against your reference sequence, so it's
possible that some traces may get assembled into their own
contigs if they differ too much.

Does this address the request sufficiently?