how can I do the assembly of contigs
Entering edit mode
14 months ago


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.

assembly contigs sequencing • 517 views
Entering edit mode
14 months ago
hugo.avila ▴ 190

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.


Login before adding your answer.

Traffic: 1746 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6