Consed? - anyone use it? (Dec/26/2008 )
Consed & its family Phred and Phrap are DNA sequence analysis programs for the LINUX environment. Is anyone familiar with them? I am running into a problem where it will generate ace files but it will not assemble, so it will not pull up any sequencing traces. How do I make it assemble or align traces so I can see my chromatograms?
i used phrephrap like 2 years ago, so my memory is not very fresh. if i remember well you will need to have your chromatograms in a specific directory and then do the base call with phred and the assembly with phrap. you could do that with a single command line specifying what is the minimum quality of each base allowed for the assembly. i'm not sure if it will actually assemble the chromatograms but i think it doesn't.
hope this helps you.