Article
Long-read mapping to repetitive reference sequences using Winnowmap2.
Nature methods - 1 Jun 2022
Jain Chirag, Rhie Arang, Hansen Nancy F, Koren Sergey, Phillippy Adam M
Abstract excerpt
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that...
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