Perhaps a few of the list have experience with both STADEN and Consed (phred/phrap/consed, http://www.phrap.org/\). I would like to know your opinion about how they compare to each other for genome assembly and editing/analysis. My impression is that consed is harder to set up (there is no installer package), but more powerful and flexible than STADEN.
Naturally I'm biased :-)
But when comparing Consed to Gap4, be careful to compare just Consed to just Gap4. My own gut feeling is that Phred obviously has no competition from the Staden package. Phrap also beats Gap4's assembly hands down. But Gap4 IMO beats Consed easily IMO as an editor. Therefore mixing and matching the two packages is probably the best solition.
Where Gap4 falls down I think is in ease of getting ace files into it. We generally use the caftools package to do such things, but it can be buggy at times when faced with broken ace files (which appear to be very common).
I am using both at present, consed more than gap4 now. I like both, but I haven't tried converting my consed project .ace files into gap4 databases for gap4. I like the 'assembly view' idea in consed, where you see your contigs as rectangular blocks, and can look for sequence matches between them. Is there anything like that planned for gap4?
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