I am currently learning to use pregap and gap programs and still have many questions.
My first wonder would be, if instead of sequencing by shotgun sequences are obtained from Tn5sequencing, is there any option to first join the forward and reverse readings (and their traces) and then try to assemble them?
Also, if there isnt such an option, would it still be possible to use the pregap and gap in order to assemble them?
How should I "treat" the forward and reverse readings from the same template (since I want them to be facing away from each other).
Finally (for now), how should I name the readings?
Thank you very much on advance.
i believe this should be possible. for assembling overlapping sequence reads from either end of a cloned insert, i use a special config file and naming convention in pregap and then do a "directed assembly" in gap. a labmate gave me the config file (he obtained it from the staden authors or some other guru) and helped me through the process. so, although i don't know exactly what kind of config file you will need, i am fairly certain you can do what you want to do!