07-23-2016, 04:10 PM

I'm trying to determine what a reasonable alignment score would be, given my sequence length and expected amount of overlap.

What is the alignment scoring system employed by the illuminapairedend command?

Match score? 1?

Mismatch penalty ? -2?

Or is a complex match/mismatch scoring matrix used?

Gap penalty type? Affine?

Gap open penalty value?

Gap extend penalty value?

What is the alignment scoring system employed by the illuminapairedend command?

Match score? 1?

Mismatch penalty ? -2?

Or is a complex match/mismatch scoring matrix used?

Gap penalty type? Affine?

Gap open penalty value?

Gap extend penalty value?