Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Haplotype assembly software tools | Whole-genome sequencing data analysis

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…
G T A T C G C T A
Prism
Desktop

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…

G T A T C G C T A
HapCUT
Desktop

HapCUT

Allows haplotype assembly for diverse sequencing technologies. HapCUT is a…

Allows haplotype assembly for diverse sequencing technologies. HapCUT is a maximum likelihood based algorithm that can assemble haplotypes for a diverse array of data modalities while other tools are…

G T A T C G C T A
WhatsHap
Desktop

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.…

G T A T C G C T A
AltHap
Desktop

AltHap

Formulates haplotype assembly as sparse tensor decomposition. AltHap is a…

Formulates haplotype assembly as sparse tensor decomposition. AltHap is a haplotyping assembly method for diploid, polyploid, and polyallelic polyploid organisms. The framework exploits structural…

G T A T C G C T A
phASER
Desktop

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
HapCol
Desktop

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…

G T A T C G C T A
HapTree
Desktop

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…

G T A T C G C T A
HARSH
Desktop

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…

G T A T C G C T A
HapCHAT
Desktop

HapCHAT Haplotype Assembly Coverage Handling by Adapting Thresholds

Enables to phase high coverage Pacific Biosciences (PacBio) reads. HapCHAT…

Enables to phase high coverage Pacific Biosciences (PacBio) reads. HapCHAT contains a preprocessing step which merges reads belonging to the same haplotype based on a graph clustering method. It has…

G T A T C G C T A
Daccord
Desktop

Daccord

Computes preliminary consensus sequences for the splitting. Daccord is a…

Computes preliminary consensus sequences for the splitting. Daccord is a non-hybrid long read consensus program based on local de Bruijn graph assembly. This application contains the functions to…

G T A T C G C T A
HapCompass
Desktop

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…

G T A T C G C T A
SV-AUTOPILOT
Desktop

SV-AUTOPILOT Structural Variation AUTOmated PIpeLine Optimization Tool

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is…

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is a pipeline that can be used on existing computing infrastructure in the form of a Virtual Machine (VM) Image. It…

G T A T C G C T A
SDhaP
Desktop

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…

G T A T C G C T A
HapEdit
Desktop

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…

G T A T C G C T A
H-PoP/H-PoPG
Desktop

H-PoP/H-PoPG

Respectively solves the Polyploid Balanced Optimal Partition (PBOP) problem and…

Respectively solves the Polyploid Balanced Optimal Partition (PBOP) problem and the Optimal Partition with Genotype constraint (PBOPG) problem. H-PoP and H-PoPG are two heuristic partitioning…

G T A T C G C T A
FastHap
Desktop

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…

G T A T C G C T A
ProbHap
Desktop

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…

G T A T C G C T A
HAPLOWSER
Desktop

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,…

G T A T C G C T A
hapAssembly
Desktop

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…

G T A T C G C T A
MixSIH
Desktop

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…

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

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…

G T A T C G C T A
V-pipe
Desktop

V-pipe

Allows users to study clinical applications of next generation sequencing (NGS)…

Allows users to study clinical applications of next generation sequencing (NGS) data.

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.