Why Chromatogram Files Make Shotgun Assembly Easier

Sorry - this page really isn't written yet.

Basically, shotgun assembly with mere text sequence is difficult, since to resolve any conflicts between reads, you have to go back to the original reads and attempt to locate the conflicting positions. If you've done this, you know what a pain it can be.

Programs that can read and utilize the chromatographic trace during assembly can not only use that information to provide a better assembly, but they usually can automoatically pop up aligned traces whenever you need to resolve conflicts. A few minutes with such a program can do what you used to do in a hour with textual sequence alignments.

If you're not using a chromatographic alignment program for shotgun assembly, you are still working in the dark ages. (Note that this also means that if you are using manual sequencing data for assembly, you are *really* behind the times.)

I will try to provide additional information and example pictures in a future revision of this page.