De novo hybrid genome assembly of novel bacteria
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2.2 years ago

Hi All,

I'm currently working on a de novo genome assembly on a novel bacterium using nanopore and illumina data. I have done multiple assemblies and found that my best results came from Canu and MaSuRCA but I am now unsure of how to proceed. I believe I need to polish my assemblies and I have looked into nanopolish, medaka, and pilon but I am uncertain how to measure the success of polishing and subsequently which assembly/polish method I should proceed with afterwards. What metrics can I use for comparisons without the need for a reference genome to help accomplish this?

Thank you in advance!

Assembly nanopore illumina hybrid • 826 views
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2.2 years ago
Mensur Dlakic ★ 14k

I suggest you try multiple approaches and compare them in the end. For example, SPAdes also has a nice hybrid assembly algorithm, and you may want to consider a Unicycler pipeline that automates both assembly and polishing.

Some info about assembly quality can be found here.

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sorry for the late reply, but I followed your advice and tried unicycler and it ended up giving me some very promising results so thank you, I appreciate it!

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