Nanopore data decontamination

Question

[Juke34]

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.

[GenoMax]

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.

[Juke34]

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

[Christina]

But these tools are meant for short reads. Can they really work for Nanopore data?