how can I do the assembly of contigs

Question

[aline.paula142912]

Hi,

I have a ssequence from a sequencing that I made, but it still has a lot of gaps. I have a file with the contigs, how can I do the assembly of these contigs? I tried to use Scaffold Builder but it doesn't show me the mutations that i problably have in the sequence.

Answer 1

[hugo.avila]

Hi ! if you are working with bacteria:

You can try some in silico gap filling with GapFiller to reduce gaps and then map the remaining contigs with Mummer or Contigator onto a reference genome to get a scaffold. Also, you can make supplementary assemblies with different programs and parameters to create a database of alternative contigs. FGAP takes this contigs as references to correct gaps in the scaffold.

But before you do this methods consider if you really need a complete genome to answer your biological question. If you a have a good N50 you can work just fine with only contigs, In silico methods to close gaps do work but are prone to errors and false assumptions of genome structure.