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Viral population reconstruction software tools | High-throughput sequencing data analysis

Viral haplotype reconstruction from a set of observed reads is one of the most challenging problems in bioinformatics today. Next-generation sequencing technologies enable us to detect single-nucleotide polymorphisms (SNPs) of haplotypes-even if the…
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ShoRAH
Desktop

ShoRAH Short Reads Assembly into Haplotypes

A computational method for quantifying genetic diversity in a mixed sample and…

A computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. This approach provides…

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V-Phaser 2
Desktop

V-Phaser 2

A software package for inferring intrahost diversity within viral populations.…

A software package for inferring intrahost diversity within viral populations. V-Phaser 2 adds three major methodologies to the state of the art: (i) a technique to efficiently utilize paired end…

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RegressHaplo
Desktop

RegressHaplo

Reconstructs haplotypes using a penalized regression approach. RegressHaplo is…

Reconstructs haplotypes using a penalized regression approach. RegressHaplo is an algorithm developed to (i) split the genomic region of interest into subregions, (ii) construct local haplotypes for…

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QuRe
Desktop

QuRe

A program for viral quasispecies reconstruction, specifically developed to…

A program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) NGS data.

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EVORhA
Desktop

EVORhA EVOlutionary Reconstruction of hAplotypes

A haplotype reconstruction method that complements phasing information in the…

A haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as…

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SAVAGE
Desktop

SAVAGE Strain Aware VirAl GEnome assembly

Allows for reference-free assembly of viral quasispecies from sequencing data…

Allows for reference-free assembly of viral quasispecies from sequencing data sets of truly deep coverage. SAVAGE makes relevant contributions for (i) the construction of overlap graphs from deep…

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HaploClique
Desktop

HaploClique

A computational approach to reconstruct the structure of a viral quasispecies…

A computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.

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QuasiRecomb
Desktop

QuasiRecomb

A jumping hidden Markov model that describes the generation of the viral…

A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.

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MosaicSolver
Desktop

MosaicSolver

It determines the recombinants originating from two parent genomes, and their…

It determines the recombinants originating from two parent genomes, and their proportions, using next-generation sequencing pileup data.

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Hexahedron
Web

Hexahedron

Aims users to reconstruct local and global sequences. Hexahedron can determine…

Aims users to reconstruct local and global sequences. Hexahedron can determine relative frequency of local and global sequences. It offers a visualization technique that represents the dynamic nature…

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aBayesQR
Desktop

aBayesQR

Employs a maximum-likelihood framework to infer individual sequences in a…

Employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data. aBayesQR is an algorithm performs reconstruction of a quasispecies from…

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LayerCake
Desktop

LayerCake

A self-contained visualization tool that allows for the rapid analysis of…

A self-contained visualization tool that allows for the rapid analysis of variation in viral NGS data. LayerCake enables the user to simultaneously visualize variations in multiple viral populations…

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ViQuaS
Desktop

ViQuaS Viral Quasispecies Spectrum Reconstruction using short NGS reads

Provides a method for spectrum reconstruction. ViQuaS is an analysis pipeline…

Provides a method for spectrum reconstruction. ViQuaS is an analysis pipeline for viral Quasispecies Spectrum Reconstruction (QSR) using short next-generation sequencing (NGS) reads. This method…

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VirVarSeq
Desktop

VirVarSeq

Allows variant calling at the codon level. VirVarSeq is a low frequency virus…

Allows variant calling at the codon level. VirVarSeq is a low frequency virus variant detection pipeline that identifies true variants at the codon level within a viral population using Illumina…

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ABC-MCMC
Desktop

ABC-MCMC Approximate Bayesian Computation Markov chain Monte Carlo estimation

Infers evolutionary genetic parameters from a collection of short-read…

Infers evolutionary genetic parameters from a collection of short-read sequences obtained from a mixed sample of anonymous DNA using the frequencies of nucleotides at each site only without…

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ViVaMBC
Desktop

ViVaMBC

Explores quality scores and second best base calls for identifying and…

Explores quality scores and second best base calls for identifying and quantifying viral variants. ViVaMBC is optimized to call variants at the codon level (nucleotide triplets) which enables…

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ANDES
Desktop

ANDES ANalyses of DEep Sequencing

A software library and a suite of applications for the statistical analyses of…

A software library and a suite of applications for the statistical analyses of deep sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide…

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PredictHaplo
Desktop

PredictHaplo

This software aims at reconstructing haplotypes from next-generation sequencing…

This software aims at reconstructing haplotypes from next-generation sequencing data. A typical application example is to reconstruct HIV-1 haplotypes present in a blood sample from a patient based…

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Pooling
Desktop

Pooling

A cost-effective and reliable protocol for sequencing of viral samples, that…

A cost-effective and reliable protocol for sequencing of viral samples, that combines NGS using barcoding and combinatorial pooling and a computational framework including algorithms for optimal…

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ViSpA
Desktop

ViSpA Viral Spectrum Assembler

Implements a viral assembling and frequency estimation methods. This software…

Implements a viral assembling and frequency estimation methods. This software uses a simple error correction, viral variants assembling based on maximum-bandwidth paths in weighted read graphs and…

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