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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Assembled contigs can not be circularized #233

Open taha-lang opened 3 weeks ago

taha-lang commented 3 weeks ago

Hello, for some samples, when assembling the chloroplast genome, the two contigs do not merge into a circular contig. I'm trying to find a solution, as well as to assemble them manually if possible, if the automatic command is not available. Here's the message from the novoplasty software. LINKS BETWEEN CONTIGS

01----> 02 OR 1122512 1122512----> END_REVERSE START----> 01

------Assembled contigs can not be circularized, some sequence is probably missing!------n

parksonpurity commented 1 week ago

I have the same issues with mitogenomes. Anyone who has a solution?

taha-lang commented 1 week ago

Assembled contigs can not be circularized, some sequence is probably missing!------n Hello friends, regarding the problem of circulazid cp assembli not being circulated, I'd like to share with you the solution found in my case,. it's about the reduce ambiguous N's parameter, you put yes. Then the assembly will be merged ![Uploading Capture d’écran du 2024-09-08 11-09-58.png…]()

parksonpurity commented 1 week ago

Hi taha-lang, thanks for your reply. I did try in this way, but the same issue still popped up.