My personal feeling is that the best combination *in theory* is to use
gap4's interface to phrap and phred.
You can use phred to base call your reads anyway, regardless of
whether you use phrap to assemble them.
The problem with phrap assembly in combination with gap4 is that each
batch of new reads gets assembled into a fresh contig, not an existing
contig. This means that you then have to join the contigs by hand.
Since you want to automate this as much as possible, this can cause
Gap4's assembly engine is not as good as phrap, but I hear there are
internal developments to improve this, and James has been very helpful
to us in providing some stopgap measures.
One of the Staden package's huge strengths is in automation. Almost
all of the functionality of gap4 is available through the tcl
interface to it, stash, although there are some missing things. For
instance gap4's "shuffle pads" feature is not available through the
tcl interface, and neither is "phrap reassembly".
However, the tcl interface is nice, and I've had very little trouble
knocking together some automated processing scripts.