Flipping a DNA sequence (not reverse complementing) using command line/samtools?

Hi all,

I have BioNano Scaffolds of sequence data (no solid reference at the moment) and I am trying to orient them in the correct way to so I can do PCR and attempt to complete the sequence. One of my scaffolds is 67 MB, but I believe (based on BLATs and other context clues from the project) that this sequence is actually reversed. Is there a way using samtools or the command line to easily flip this sequence? Given that it is so big I would rather stay on the cluster and not have to download it to my computer to try and flip – but if that is what I need to do so be it.

Thanks so much!