A KL-divergence metric on inter-motif distance distributions in a centeny representation ranks the accuracy of human T2T genome assemblies at centromeres.
and Mikheenko, Alla and Vollger, Mitchell R
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An O(n log log n) time O(n) space algorithm for anchored edit distance chaining is obtained by merging gap-cost computation from Chao and Miller (1995) with overlap-cost computation from Baker and Giancarlo (1998), plus a practical O(n log n) implementation.
The anti-lexicographic SUS-anchor achieves sampling densities less than 1% above the lower bound for alphabet size 4 and k=1, substantially outperforming bidirectional anchors.
citing papers explorer
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A mathematical framework for centromere-aware evaluation of human genome assemblies
A KL-divergence metric on inter-motif distance distributions in a centeny representation ranks the accuracy of human T2T genome assemblies at centromeres.
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Revisiting $O(n \log \log n)$ chaining for anchored edit distance
An O(n log log n) time O(n) space algorithm for anchored edit distance chaining is obtained by merging gap-cost computation from Chao and Miller (1995) with overlap-cost computation from Baker and Giancarlo (1998), plus a practical O(n log n) implementation.
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The anti-lexicographic SUS-anchor: a near-optimal k=1 sampling scheme
The anti-lexicographic SUS-anchor achieves sampling densities less than 1% above the lower bound for alphabet size 4 and k=1, substantially outperforming bidirectional anchors.