Is your feature request related to a problem? Please describe
A new publication was just published describing more in-depth parameter modelling to find the most optimal paramaters for mapping with a range of mappers.
Of note they find the best parameters for BWA are turnning of seeding, -n 0.01, and a gap -o 2. I also just noted this is also what was selected by the old as F Mammoth
Describe the solution you'd like
Consider updating default mapping paramaters to reflect the above, and add the gap parameter
Describe alternatives you've considered
Leave it as it is, as the papers don't disagree and we don't know which is best.
Additional context
Is your feature request related to a problem? Please describe
A new publication was just published describing more in-depth parameter modelling to find the most optimal paramaters for mapping with a range of mappers.
Of note they find the best parameters for BWA are turnning of seeding,
-n 0.01, and a gap-o 2. I also just noted this is also what was selected by the old as F MammothDescribe the solution you'd like
Consider updating default mapping paramaters to reflect the above, and add the gap parameter
Describe alternatives you've considered
Leave it as it is, as the papers don't disagree and we don't know which is best.
Additional context