Question: De novo hybrid genome assembly of novel bacteria
gravatar for tmurphy201596
11 months ago by
tmurphy2015960 wrote:

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!

ADD COMMENTlink modified 11 months ago by Mensur Dlakic5.8k • written 11 months ago by tmurphy2015960
gravatar for Mensur Dlakic
11 months ago by
Mensur Dlakic5.8k
Mensur Dlakic5.8k wrote:

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.

ADD COMMENTlink written 11 months ago by Mensur Dlakic5.8k

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!

ADD REPLYlink written 10 months ago by tmurphy2015960
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