Enhancement: Using LAST-TRAIN scores with minimap2

[harisankarsadasivan]

Hi, I'm working on a modified dataset with a noise profile different from standard ONT and used LAST-TRAIN to train scoring parameters to map 90% reads. Directly applying these indel scoring parameters & average substitution param to minimap2 does not yield results. I was thinking if it is possible to include a method to plug-in the LAST trained substitution matrix to minimap2. I think the other indel scoring parameters can be directly plugged in at the moment.

[lh3]

What is the scoring matrix?

[harisankarsadasivan]

@lh3 , thank you for your very prompt response.The scoring parameters I got after training is as follows: #last -a 8 #last -A 11 #last -b 6 #last -B 3 #last -s 1 #last -S 1

score matrix (query letters = columns, reference letters = rows):

   A      C      G      T

A 7 -11 -9 -2 C -12 7 -5 -12 G -6 -3 4 -5 T -1 -12 -5 3

[harisankarsadasivan]

@lh3 Kindly give me a heads-up, if you are planning for this or not. If not, I can try and do this now. Would happily welcome any useful pointers or tips you have on the edits to be made.