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illuminapairedend: alignment scoring system?
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?
Illuminapaired end score system is described in the obitools article

Boyer F, Mercier C, Bonin A et al. (2016) obitools: a unix-inspired software package for DNA metabarcoding. Molecular ecology resources, 16, 176–182.
Hi Eric,

I'm probably a little slow on the uptake, but it seems that only the weighting system by quality score is discussed in Boyer et al 2016.

"The score associated with a pair of nucleotides in the alignment is a linear combination of a match reward and of a mismatch penalty weighted by" pmatch and pmismatch

After calculating the weights, what "match reward" or "mismatch penalty" do the weights modify?



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