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.