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Denovo assembly of bacterial genome

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

assembly
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updated by colindaven colindaven • written by th526 • th526

2 answers

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

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written by Sej Modha Sej Modha

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

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written by colindaven colindaven

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