Reverse and Forward assembly using Phrap

Guy Champagne champagneg50 at hotmail.com
Thu Jan 10 12:44:55 EST 2002


Hello

I'm succesfully using Phred and Phrap within the Staden package for a
while for shotgun assembly projects.

Now I want to simply assemble the Forward and Reverse read of
individual clone (assemble 2 by 2 instead of all reads together). By
doing this I have the strange result that the good quality sequence
and the bad quality sequence are reverse meaning that the good
sequence (higher phred score) are in dark grey and the bad in light
grey.

Whith the same reads if I'm using a shotgun assembly (phrap with all
readings instead of only Forward and reverse)the quality clipping
perform by phrap is Okay (Goog quality sequences are in light grey)

Did someone had face this problem before ?

Thanks for your help

Guy Champagne
Biology Department
McGill University




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