How to pass minimap2 parameters?

[evo-eco-gen]

Hi,

I ran the following command hoping to get a .paf with CIGAR strings (to then convert into .delta): RagTag took 20x longer, but did not return the CIGAR... Could you provide an example of how to pass minimap2 parameters, please?

ragtag.py scaffold my_ref my_query -f 1000 -q 10 -d 100000 -i 0.2 -a 0.0 -s 0.0 -g 100 -m 1000000 --remove-small -u \ --mm2-params '-c -t12'

[malonge]

I can't explain this, especially if it did take longer to run. Perhaps use double quotes?

Anyways at least you can just generate the paf file how ever you want independently. Instructions here.