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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.
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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.
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.
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.
The text was updated successfully, but these errors were encountered: