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StevenWingett / FastQ-Screen

Detecting contamination in NGS data and multi-species analysis
https://stevenwingett.github.io/FastQ-Screen/
GNU General Public License v3.0
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Processing very long reads #34

Open StevenWingett opened 4 years ago

StevenWingett commented 4 years ago

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 commented 3 years ago

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 commented 2 years ago

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.