best practices documentation on the ONT long reads

[yinshiyi]

This link is referred many times in this forum as the best practice when analyzed ONT with Minimap2
https://combine-lab.github.io/salmon-tutorials/2021/ont-long-read-quantification/
eg. #924, #790

I would like to suggest some clarification regarding it. I am posting my ideas here, because I can't find a way to access salmon-tutorials repo.

1. the choice of -Y flag when created minimap references:
   I think the -Y should be used during alignment, not during reference creation.
   https://lh3.github.io/minimap2/minimap2.html
2. the ErrorModel choice
   The ONTAlignmentModel documentation is hard to find. But based on my understanding
   --ont --noErrorModel is not the same as --ont, in the 2021 guide, it is comparing --ont against --noErrorModel.

Other minior suggestions

3. the salmon -la flag explaination
   The not immediately clear regarding this flag. I think it is a combination of the -l (library choice auto) and -a (alignment file). Perhaps it is worthy to add a brief description to the documentation.
4. -ax map-ont usage
   credit Quantification of direct RNA seq reads (ONT) using salmon #786
   The guide used -a -x map-ont flag in minimap2 which I think it is equivalent to -ax map-ont. It is perhaps a simple concept for others, but it take me a bit to follow. Perhaps it is worthy to add a brief description to the documentation.