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illuminapairedend: alignment scoring system?
#1
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?
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#2
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.
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#3
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?

Thanks!

Chris
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