Processing very long reads

[StevenWingett]

Devise a way to handle very long reads (e.g. Oxford Nanopore).

Maybe make compatible with Minimap2 - as discussed by email with users. Alternatively, break up reads and process with Bowtie/Bowtie2

[s-andrews]

Just had another request in for this, asking for minimap2 as an option for the back end. I know Felix implemented this in bismark and it was fairly straight forward so it might not be too hard to add.

[adknaupp]

I would like to see the minimap2 backend implemented so I can use FastQ screen to filter human contamination out of PacBio data. I have years of runs I could potentially screen as I work in a center with two PacBio Sequel II instruments. If given a couple pointers, I would be willing to implement the necessary functionality myself.