Minimap preset option

[annabel-dekker]

Is your feature related to a problem?

We are testing your pipeline for our nanopore sequencing. However, we have an in-house solution that uses a form of rolling circle amplification to improve the quality of our reads. What we notice is that we can validate the kraken2 classifications, but the classifications of minimap2 are sometimes really poor (lots of false positives and poor mapping). We are wondering whether this might be due to the preset for map-ont (-x).

Describe the solution you'd like

The possibility to change the preset for minimap2 to test whether your pipeline can be used for different input data as well.

Describe alternatives you've considered

I could test this myself of course by digging through the workfolders and adjusting some code on the fly :), if I managed I will let you know if this made an impact.
Thanks again for thinking along in advance!

Additional context

No response

[nggvs]

Hi @annabel-dekker ,
Thank you for your suggestion, if I understand it right you'd like to have minimap2 preset as a parameter no? I'd made an internal ticket to consider it in future releases.
Thank you for using the workflow and for your feedback!

[annabel-dekker]

I tested a manual run of minimap2 with -x map-hifi instead of map-ont; and as expected makes a huge difference in classification for our high quality nanopore reads. It would be very much appreciated to include this parameter in the next releases, so that we can test it better! :) Thanks a lot!

[nggvs]

Hi @annabel-dekker ,
I have created a ticket to consider this feature for feature releases.
Thank you very much for using the workflow and for your feedback!

[nggvs]

Closing as it has been raised internally in a ticket