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Variant visualization software tools | Whole-genome sequencing data analysis

There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats.Source text:(Preston et al., 2012) VarB: a…
IGV
Desktop

IGV Integrative Genomics Viewer

A high-performance viewer that efficiently handles large heterogeneous data…

A high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of…

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ProteinPaint
Web

ProteinPaint

Enables data visualization and cross-study comparison for the broad genetic…

Enables data visualization and cross-study comparison for the broad genetic research community. ProteinPaint is a visualization application designed to deliver a premium visualization experience with…

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MutationMapper
Web

MutationMapper

Interprets mutations with protein annotations. MutationMapper is a…

Interprets mutations with protein annotations. MutationMapper is a vizualisation tool provided by cBioPortal, a platform designed to lower the barriers of access to the complex data sets and thereby…

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OncoPrinter
Web

OncoPrinter

Generates oncoprints from user’s data. OncoPrinter is a vizualisation tool…

Generates oncoprints from user’s data. OncoPrinter is a vizualisation tool provided by cBioPortal, a platform designed to lower the barriers of access to the complex data sets and thereby…

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BamView
Desktop

BamView

An interactive Java application for visualizing the large amounts of data…

An interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. BamView supports the BAM (Binary…

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SVPV
Desktop

SVPV Structural Variant Prediction Viewer

Presents a visual summary of the most relevant features for structural variant…

Presents a visual summary of the most relevant features for structural variant (SV) prediction from whole genome sequencing (WGS) data. SVPV allows users to visualise SV together, along with…

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Highlander
Desktop

Highlander

A Java software coupled to a local database to centralize all variant data and…

A Java software coupled to a local database to centralize all variant data and annotations from the lab, and to provide powerful filtering tools that are easily accessible to the biologist. Data can…

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RareVariantVis
Desktop

RareVariantVis

A tool for analysis of genome sequence data (including non-coding regions) for…

A tool for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants. It visualizes variants along their respective chromosomes, providing information…

BioCircos.js
Desktop

BioCircos.js

An interactive and lightweight JavaScript library especially for biological…

An interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js is not a web application for end-users but a JavaScript library for…

Savant
Desktop

Savant

A next-generation genome browser designed for the latest generation of genome…

A next-generation genome browser designed for the latest generation of genome data.

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GENESIS
Web

GENESIS

Provides a cloud-based system that allows users to directly process and analyze…

Provides a cloud-based system that allows users to directly process and analyze next-generation sequencing (NGS) data through a user-friendly graphical user interface (GUI). The first objectives of…

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VarB
Desktop

VarB

Visualizes (un)phased polymorphisms in a VCF file by sample, genetic region and…

Visualizes (un)phased polymorphisms in a VCF file by sample, genetic region and quality. The basic inputs are a reference genome (fasta), variant (VCF) and annotation (gff) files. Complete genomes or…

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Panoptes
Desktop

Panoptes

Focuses on supporting genetic data in the context of rich metadata. Panoptes is…

Focuses on supporting genetic data in the context of rich metadata. Panoptes is an open source framework for collaborative exploration of large-scale genomes variation dataset. It includes some…

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BPS
Desktop

BPS BreakPoint Surveyor

Examines breakpoint predictions, together with their associated structural…

Examines breakpoint predictions, together with their associated structural variation and gene context. BPS is a pipeline for integrating large, complex data sets with a scalable architecture…

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svviz
Desktop

svviz

A sequencing read visualizer for structural variants (SVs) that sorts and…

A sequencing read visualizer for structural variants (SVs) that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads,…

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Meander
Desktop

Meander

A tool to visualize read-depth and pair-end information as it originally comes…

A tool to visualize read-depth and pair-end information as it originally comes from NGS machines at various resolutions. Its main purpose is to provide intuitive visualizations for an easier…

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CNView
Desktop

CNView

A software tool for normalized visualization, statistical scoring, and…

A software tool for normalized visualization, statistical scoring, and annotation of CNVs from population-scale whole-genome sequencing (WGS) datasets. CNView has six sequential steps: (1) matrix…

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SVAMP
Desktop

SVAMP

A standalone desktop application to visualise variants (SNPs and indels) and…

A standalone desktop application to visualise variants (SNPs and indels) and perform real-time analysis on selected regions of a genome on specific samples. SVAMP has some interesting features like…

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RaggedExperimen…
Desktop

RaggedExperiment

Provides a flexible representation of copy number, mutation, and other data…

Provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. RaggedExperiment is an R package that allows for ragged…

TASUKE
Desktop
Web

TASUKE

A web application that visualizes large-scale resequencing data generated by…

A web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and…

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Torrent Suite…
Server

Torrent Suite Software

Allows users to perform customized and automated data analysis, as well as to…

Allows users to perform customized and automated data analysis, as well as to store data.

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PDB2Genome
Desktop

PDB2Genome

Adds aligned protein data bank (PDB) data as tracks in such a visualization…

Adds aligned protein data bank (PDB) data as tracks in such a visualization would help reveal relationships between protein structures and single nucleotide polymorphisms (SNPs), including small…

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Batch…
Web

Batch Insertion Viewer

Generates a batch report for insertions of interest for Drosophila…

Generates a batch report for insertions of interest for Drosophila melanogaster. Users need only to paste the insertion name, insertion point and chromosome.

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vcf.iobio.io
Web

vcf.iobio.io

Examine your variant file in seconds. vcf.iobio.io is a variant data inspector…

Examine your variant file in seconds. vcf.iobio.io is a variant data inspector tool that quickly samples vcf files and visualizes a series of metrics.

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CNVineta
Desktop

CNVineta

Analyzes copy number variation (CNV) data from large datasets. CNVineta is a…

Analyzes copy number variation (CNV) data from large datasets. CNVineta is a package composed of appliances to detect and visualize common CNVs for a phenotype of interest and disease-associated rare…

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VCS
Web

VCS Visualization of CNV or SNP

Provides a graphical view of the physical distribution of Copy number variation…

Provides a graphical view of the physical distribution of Copy number variation (CNV) or single nucleotide polymorphism (SNP) on chromosomes. VCS is an online application that shows the enrichment…

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