Question: Tool to flip contigs the right orientation with respect to a reference sequence
0
gravatar for Tonor
3 months ago by
Tonor420
UK
Tonor420 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 • 173 views
ADD COMMENTlink modified 3 months ago by h.mon15k • written 3 months ago by Tonor420
2
gravatar for h.mon
3 months ago by
h.mon15k
Brazil
h.mon15k wrote:

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

ADD COMMENTlink written 3 months ago by h.mon15k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2030 users visited in the last hour