Question: Tool to flip contigs the right orientation with respect to a reference sequence
0
gravatar for Tonor
2.7 years ago by
Tonor430
UK
Tonor430 wrote:

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.

alignment sequence assembly • 963 views
ADD COMMENTlink modified 2.7 years ago by h.mon31k • written 2.7 years ago by Tonor430
2
gravatar for h.mon
2.7 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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

ADD COMMENTlink written 2.7 years ago by h.mon31k
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