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Update to sourmash Nodegraph instead of khmer to allow for computation of minimum read length #77

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olgabot opened this issue Jun 1, 2020 · 1 comment
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olgabot commented Jun 1, 2020

With this PR: sourmash-bio/sourmash#1009 - the sourmash Nodegraph now becomes more appealing to use instead of khmer's Nodegraph. This is because the n_unique_kmers attribute that is now added, allows for computation of the minimum necessary read length for a given false positive rate with this equation:

Screen Shot 2020-05-29 at 2 06 53 PM

@olgabot olgabot added this to the v1.1.0 milestone Jun 1, 2020
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olgabot commented Jul 28, 2020

This is low-hanging fruit for speeding up the module, but backwards compatibility may be tricky for older bloom filters. There's probably a fairly straightforward try/except thing to use here, though.

@olgabot olgabot mentioned this issue Jul 28, 2020
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