Question: Break the assembled genome by error-some regions !
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gravatar for BioGeek
12 months ago by
BioGeek140
BioGeek140 wrote:

How to break the assembled genome by error-some regions? I map ONT reads against the genome and it return many misaligned regions, how to break the genome into fragment on those regions ?

ont error breaks assembly genome • 294 views
ADD COMMENTlink written 12 months ago by BioGeek140

Can you add additional clarification on what you are trying to do? Is the genome assembled from the same reads you are using? If it was then how did you do the assembly? What program did you use?

how to break the genome into fragment on those regions ?

What do you mean by this bit?

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax70k

Falcon were used to assemble the genome. After mapping, I notice such cases https://dazzlerblog.files.wordpress.com/2017/04/screen-shot-2017-04-18-at-9-54-01-am.png

I wanted to break the genome by those "error-some" regions (by middle of X and Y in the figure) and re-scaffold them. How to break the assembled genome my such regions ?

ADD REPLYlink written 12 months ago by BioGeek140

So the non-white lines in the image are sequences that should not be there (or you are not interested in)? Is that leftover adapter contamination that was somehow incorporated in the assembly?

ADD REPLYlink written 12 months ago by genomax70k

Hey BioGeek,

Have you carried out any filtering, trimming or adapter cleaning on the raw ONT reads? It is recommended to do some basic cleaning on the reads before aligning/assembling them. You could use tools like nanofilt or Porechop for ONT reads QC.

ADD REPLYlink modified 12 months ago • written 12 months ago by Sej Modha4.3k
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