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Picking values of k #20

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standage opened this issue Dec 22, 2016 · 1 comment
Closed

Picking values of k #20

standage opened this issue Dec 22, 2016 · 1 comment

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@standage
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In addition to picking appropriate memory sizes, there's also the question of picking an appropriate value of k. For the human stuff we're currently limited by khmer's maximum of 32, but that should be solved very soon.

@standage
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We have had support for arbitrarily large k sizes for a while now, but I just recently revisited the question of picking a k value. For simulated reads at 30x coverage, I ran the entire kevlar workflow at k={27,31,35,39,43,47,51}. ROC curves shown below.

kevlar-ksizes-combined

The differences are minor, and the k=31 default I've been using for a while seems to strike a good balance across the different variant classes.

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