De novo hybrid genome assembly of novel bacteria

Question

[tmurphy201596]

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!

Answer 1

[Mensur Dlakic]

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.

[tmurphy201596]

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!