WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome (2019, methodology): “The DeepVariant callset from the full 28-fold coverage data was phased using WhatsHap v.0.17 (whatshap phase) with the subsampled alignments.”
Long-read human genome sequencing and its applications (2020, neutral): “…methods that take advantage of the inherent phasing present in long-read data (such as FALCON-Unzip) 75 and methods that apply orthogonal technologies to phase single-nucleotide polymorphisms in long-read data (such as Strand-seq 9,88,89 , Hi-C 90 and, in the past, 10x Genomics 9 ) (Fig.”
Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021, background): “StrandphaseR ( 70 ), SaaRclust ( 71 ), and WhatsHap ( 72 , 73 ) partitioned long reads into haplotypes to generate phased genome assemblies ( 3 ).”
WhatsHap: fast and accurate read-based phasing (2016, methodology): “We summarize here the core algorithm from [14].”