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How to fix this this tangle in my bacterial genome assembly

Hi,

I am new to the genome assembly space. I have recently tried to assemble a bacterial genome and the resulting assembly graph looks like this: https://imgur.com/a/BHxtjFG

4.2Mb of it seems correctly assembled, but there is a 6kb or 12kb region, probably repetitive, that is tangled and unresolved.

I'm wondering what I should do at this stage?

Does anyone have any tips or resources for best practices for manual curation of genomes.

misassembly assembly genomics ngs
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written by Mark • Mark

I'm wondering what I should do at this stage?

Was this assembly done with short or long reads? If no long reads were used then doing some nanopore sequencing should be able to resolve the repeat assembly issue.

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written by GenoMax GenoMax

I should have mentioned that the assembly was performed with only nanopore reads. I was just wondering if anything could be done through manual curation or if more sequencing coverage was just needed

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written by Mark • Mark

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