Haplotypes play a crucial role in genetic analysis and have many applications such as gene disease diagnoses, association studies, ancestry inference and so forth. The development of DNA sequencing technologies makes it possible to obtain haplotypes from a set of aligned reads…
Desktop app
G T A T C G C T A HapCUT HapCUT

HapCUT

A max-cut based algorithm for haplotype assembly using sequence reads from the…

A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. HapCUT can be applied to sequence data generated from next-generation sequencing…

Desktop app
G T A T C G C T A HAplotype inference… HAplotype inference using Reference and…

HARSH HAplotype inference using Reference and Sequencing tecHnology

An efficient method that combines multi-SNP read information with reference…

An efficient method that combines multi-SNP read information with reference panels of haplotypes for improved genotype and haplotype inference in sequencing data. Unlike previous phasing methods that…

Desktop app
G T A T C G C T A HapCompass HapCompass

HapCompass

An algorithm for haplotype assembly of densely sequenced human genome data. The…

An algorithm for haplotype assembly of densely sequenced human genome data. The HapCompass algorithm operates on a graph where single nucleotide polymorphisms (SNPs) are nodes and edges are defined…

Desktop app
G T A T C G C T A WhatsHap WhatsHap

WhatsHap

A software tool for phasing genomic variants using DNA sequencing reads, also…

A software tool for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. WhatsHap is a fixed parameter tractable (FPT) approach with coverage as the parameter.…

Desktop app
G T A T C G C T A phasing and Allele… phasing and Allele Specific Expression from…

phASER phasing and Allele Specific Expression from RNA-seq

A fast and accurate approach for phasing variants that are overlapped by…

A fast and accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA-sequencing (RNA-seq), which often span multiple exons due to splicing. phASER…

G T A T C G C T A Hap-seqX Hap-seqX

Hap-seqX

A method for inferring haplotypes from sequence data utilizing information from…

A method for inferring haplotypes from sequence data utilizing information from both the reads and a reference dataset. Hap-seqX significantly improves current state of the art methods such as IMPUTE…

Desktop app
G T A T C G C T A FastHap FastHap

FastHap

A fast and accurate haplotype reconstruction approach, which is up to one order…

A fast and accurate haplotype reconstruction approach, which is up to one order of magnitude faster than the state-of-the-art haplotype inference algorithms while also delivering higher accuracy than…

Desktop app
G T A T C G C T A HAPLotype brOWSER HAPLotype brOWSER

HAPLOWSER HAPLotype brOWSER

A comparative browser to compare haplotypes inferred from genome assemblies or…

A comparative browser to compare haplotypes inferred from genome assemblies or metagenome assemblies. HAPLOWSER offers a convenient way to navigate haplotype sequences and functional annotations,…

Desktop app
G T A T C G C T A HapCol HapCol

HapCol

A fast and memory-efficient method for haplotype assembly from long gapless…

A fast and memory-efficient method for haplotype assembly from long gapless reads. HapCol implements a fixed-parameter algorithm for the k-constrained Minimum Error Correction problem (k-cMEC), a…

Desktop app
G T A T C G C T A Prism Prism

Prism

A haplotyping algorithm. Prism proceeds in two stages. First, in a local stage,…

A haplotyping algorithm. Prism proceeds in two stages. First, in a local stage, it assembles fragments into haplotype blocks by connecting them together at their overlapping heterozygous SNVs. This…

Desktop app
G T A T C G C T A ProbHap ProbHap

ProbHap

A software package for reconstructing parental haplotypes from long reads.…

A software package for reconstructing parental haplotypes from long reads. ProbHap works best with very long reads at a relatively shallow coverage (<= 12X). The main algorithmic idea of ProbHap…

Desktop app
G T A T C G C T A MixSIH MixSIH

MixSIH

A probabilistic model for solving the haplotype assembly problem. The model has…

A probabilistic model for solving the haplotype assembly problem. The model has two mixture components representing two haplotypes. Based on the optimized model, a quality score is defined, which we…

Desktop app
G T A T C G C T A hapAssembly hapAssembly

hapAssembly

An approach to finding optimal solutions for the haplotype assembly problem…

An approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model. This is the first time that optimal haplotypes under the MEC model are…

Desktop app
G T A T C G C T A SDhaP SDhaP

SDhaP

A framework for diploid/polyploid haplotype assembly from high-throughput…

A framework for diploid/polyploid haplotype assembly from high-throughput sequencing data. The method formulates the haplotype assembly problem as a semi-definite program and exploits its special…

Desktop app
G T A T C G C T A HapTree HapTree

HapTree

A maximum-likelihood estimation framework for polyploid haplotype assembly of…

A maximum-likelihood estimation framework for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing…

Desktop app
G T A T C G C T A HapEdit HapEdit

HapEdit

An accuracy assessment tool to view haplotype assemblies by massively parallel…

An accuracy assessment tool to view haplotype assemblies by massively parallel sequencing technologies and edit misassembled haplotypes. HapEdit offers a graphical user interface to navigate…

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