Denovo assembly of bacterial genome

Question

[th526]

Hi, I have done denovo assembly of Salmonella genome using SPAdes. I want to order the contigs and close the gap and finish the genome assembly. Could anyone suggest how to order contigs and close genome assembly. Even reference based genome assembly and finishing the final assembly is also welcome.

Regards Thippesh

Answer 1

[Sej Modha]

Mauve can be used to reorder contigs. You can also use a reference guided scaffolder such as scaffold builder to generate a draft genome assembly

Answer 2

[colindaven]

I have used Medusa for this: https://github.com/combogenomics/medusa