Hello! I'm trying to assemble some plasmid vectors that contain two repetitive regions (with around 500 and 250 bp) and it is being hard to get the complete sequence. If someone knows a better program, I'll test!
Honestly if your reads are shorter than the repetitive regions then I don't think it's a problem you can solve bioinformatically, because there's no data the software can reliably use to extend the contig.
The good news is 250-500 bp is well within the range of Sanger sequencing, and would probably be very cheap to do.
Hi!
You can either go for Sanger sequencing (after selecting the right primers that would anneal to the backbone of your vector, and allow you to sequence the insert), or try to play around with different assemblers, and see what you get (though, the first approach is by far better).
Try plasmidSPAdes (spbu.ru/software/plasmid-spades/), or Unicycler (github.com/rrwick/Unicycler)
Good luck!
Thanks, guys! My colleagues have chosen NGS sequencing because it's around 50 plasmids and little information was available about them. I actually got a better assembly now using DISCO changing the default parameters.
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