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...riant calls made from PacBio HiFi datasets. Key features relative to other phasing tools include: * Joint phasing of small variants and structural variants

...hasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works

...nitude speedup and better accuracies compared to other polyploid haplotype phasing algorithms.

...polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code hav

Phasing and SV Calling Pipeline

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

* FALCON-Phase to extend phasing between unzipped haplotig blocks (requires HiC data)

BEAGLE's methods for imputing ungenotyped markers and phasing parent-offspring trios are described in * S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using local

...is improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts

Jia K, Wang Z, Wang L et. al. SubPhaser: A robust allopolyploid subgenome phasing method based on subgenome-specific k-mers [J]. New Phytologist, 2022, in pr

Loter can be used for haplotype phasing and local ancestry inference.

...lenz, Sergey Koren, Adam M. Phillippy, Merqury: reference-free quality and phasing assessment for genome assemblies, bioRxiv (2020).]

...E version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009.

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information available. The progr

...ccurate genotype imputation in genome-wide association studies through pre-phasing. Nature Genetics 2012.

...ion of other candidate sites sharing reads. Subsequently, it performs read phasing, and carries out local realignment of each set of phased reads and the set

...ficient tiered haplotype model to improve accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haploty

...ee the iced python package for more information). Finally, HiC-Pro can use phasing data to build allele-specific contact maps.

SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. The version 4 is a refact