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I have assembled a BAC dataset (92 kb BAC, 1035 reads from an ABI3700 sequencer) once using gcphrap in GAP4 and once using phrap in standalone version.
Both times the reads were Phred base-called and the Phrap default parameters were used.
I have expected the results to be about identical but to my astonishment they were pretty different. I have to add that this BAC is a highly repetitive barley BAC (close to 90% repetitive, various retrotransposons) and in the results many repetitive regions were arranged in different contigs.
Does this comply with your experiences, are results obtained with gcphrap and phrap alone different?
Thanks for your feedback,
Not a lot of chatter on this list (or biosci). I've just been using gcphrap with gap4 and found that it doesn't align repetitive sequence very well. Haven't compared phrap with it (not sure how).
On another matter; is consed better/worse than gap4 for editing?
Regards, Mike D-S
I've no idea why it would differ. Maybe one test is to do repeat runs of both gcphrap and phrap to see whether there's any randomness in phrap itself (I've seen similar cases in other programs, oddly enough).