Tool to flip contigs the right orientation with respect to a reference sequence

Question

[Tonor]

Does anyone know a tool(s) that can flip contigs generated from a de novo assembly so that they are the correct orientation with respect to a reference sequence?

I have multiple contigs generated from de novo, blasting them identifies a few that match a particular species I'm interested in, I then want to align those contigs to the species RefSeq sequence, but some are the wrong orientation. So just wondering if anyone knows of any tools that will do this automatically, I can right a script to parse the blast output and flip sequences or use the alignment, but thought there must be something that can do this already.

Answer 1

[h.mon]

Mauve contig mover, SynMap synthenic path assembly, CG-CAT r2cat or treecat, ABACAS from PAGIT, Chromosomer.