Question: Nanopore data decontamination
2
gravatar for Juke34
4 months ago by
Juke344.1k
Sweden
Juke344.1k wrote:

Hi !

I have Nanopore data from a plant and I know there is bacterial contamination. I'm looking for an easy way to remove the contaminant. I don't find any clear tutorial explaining how to do so step by step for any of the approach below:
- I know there is a way to do so with kraken2 but it is quite slow.
- I could probably do it using diamond + Megan
- I could use Minimap2 but works only if my contaminant is a specific organism
- I thought using sourmah thinking it would be quick. I was super happy to find this tutorial (http://ivory.idyll.org/blog/2018-detecting-contamination-in-long-read-assemblies.html) but finally it is super slow.... I tried to improve the code successless...

Any help would be appreciated.

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by Juke344.1k

Do you have a reference (or a close relative) for the plant? I would select the plant reads and try to leave the bacteria behind.

You could also use kraken or kaiju provided and use those as rough stand in for bacteria.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax84k

No real close relative for the plant. And no reference.... de-novo project. Right I forgot about kaiju, will try to see what can be done with it

ADD REPLYlink written 4 months ago by Juke344.1k
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