The rapid growth of next-generation sequencing (NGS) technologies has led to a wide variety of short read DNA datasets. Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data.

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…

IGB
Desktop

IGB Integrated Genome Browser

An easy-to-use, highly customizable genome browser you can use to view and…

An easy-to-use, highly customizable genome browser you can use to view and explore genomic data and annotations, especially RNA-Seq and ChIP-Seq data sets. IGB supports real-time zooming and panning…

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SAMtools tview
Desktop

SAMtools tview

A very simple text alignment viewer based on the GNU ncurses library. SAMtools…

A very simple text alignment viewer based on the GNU ncurses library. SAMtools tview works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base…

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Tablet
Desktop

Tablet

A lightweight, high-performance graphical viewer for next-generation sequence…

A lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations…

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Consed
Desktop

Consed

A program for viewing and editing assemblies prepared by the Phrap assembly…

A program for viewing and editing assemblies prepared by the Phrap assembly program. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer,…

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BAMseek
Desktop

BAMseek

A large file viewer for BAM and SAM alignment files. BAMseek allows you to open…

A large file viewer for BAM and SAM alignment files. BAMseek allows you to open and browse SAM and BAM alignment files, no matter how large the files may be. BAMseek does not require command line…

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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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LookSeq
Web

LookSeq

A web-based application for alignment visualization, browsing and analysis of…

A web-based application for alignment visualization, browsing and analysis of genome sequence data. LookSeq supports multiple sequencing technologies, alignment sources, and viewing modes; low or…

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MagicViewer
Desktop

MagicViewer

Easily visualizes short read mapping, identify and annotate genetic variation…

Easily visualizes short read mapping, identify and annotate genetic variation based on the reference genome. MagicViewer provides a user-friendly environment in which large-scale short reads can be…

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Bambino
Desktop

Bambino

A variant detector and graphical alignment viewer for next-generation…

A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes…

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NGSView
Desktop
Web

NGSView Next Generation Sequence View

A generally applicable, flexible and extensible next-generation sequence…

A generally applicable, flexible and extensible next-generation sequence alignment editor. NGSView allows for visualization and manipulation of millions of sequences simultaneously on a desktop…

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STAR
Web

STAR Systems Transcriptional Activity Reconstruction

Aims to provide an integrated solution for both visualization and analysis of…

Aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets. STAR represents a next-generation data exploration…

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Samscope
Desktop

Samscope

A lightweight SAM/BAM file viewer that makes visually exploring next generation…

A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive. The extensive pre-processing and fast OpenGL interface of SAMSCOPE provides instantaneous…

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trackViewer
Desktop

trackViewer

Visualizes mapped reads along with annotation as track layers for next…

Visualizes mapped reads along with annotation as track layers for next generation sequencing (NGS) dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, single nucleotide polymorphisms (SNPs) and…

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Girafe
Desktop

Girafe

Facilitates the functional exploration of alignments of sequence reads from…

Facilitates the functional exploration of alignments of sequence reads from next-generation sequencing (NGS) data to a genome. Girafe allows users to investigate the genomic intervals together 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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bam.iobio
Web

bam.iobio

An open-source dashboard web application providing an insightful overview of…

An open-source dashboard web application providing an insightful overview of the contents of these large, non–human-readable BAM files and enabling users to further analyze their alignments, all in…

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VING
Desktop
Web

VING

A standalone R script that takes as input NGS mapping files and genome…

A standalone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple…

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Alview
Desktop
Web

Alview Alignment Viewer

A compiled to native architecture software tool for visualizing the alignment…

A compiled to native architecture software tool for visualizing the alignment of sequencing data. Areas with systematic read errors can be quickly identified, and inefficient attempts to verify…

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HapFlow
Desktop

HapFlow

A python application for visualising haplotypes present in sequencing data.…

A python application for visualising haplotypes present in sequencing data. HapFlow identifies variant profiles present and reads and creates an abstract visual representation of these profiles to…

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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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Bio-samtools
Desktop

Bio-samtools

A flexible and easy to use interface that programmers of many levels of…

A flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format. bio-samtools 2 provides new classes for…

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PyBamView
Web

PyBamView

A python-based application that allows you to view BAM sequence alignments…

A python-based application that allows you to view BAM sequence alignments through your web browser. PyBamView was inspired by the samtools tview tool, and was motivated by the need to better…

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SMRT View
Desktop

SMRT View

An open source Genome Browser that visualizes data generated by PacBio®…

An open source Genome Browser that visualizes data generated by PacBio® Sequencing Systems. You can explore and interact with all types of analysis results, including resequencing, de novo, cDNA,…

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ReadXplorer
Desktop

ReadXplorer

A freely available comprehensive exploration and evaluation tool for NGS data.…

A freely available comprehensive exploration and evaluation tool for NGS data. ReadXplorer extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads.…

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GenoViewer
Desktop

GenoViewer

A highly user-friendly, easy-to-operate SAM/BAM viewer and aligner tool.…

A highly user-friendly, easy-to-operate SAM/BAM viewer and aligner tool. GenoViewer enables fast and efficient NGS assembly browsing, analysis and read mapping. It is highly customized, making it…

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Golden Helix…
Desktop

Golden Helix GenomeBrowse

Delivers stunning visualizations of your genomic data that give you the power…

Delivers stunning visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an intuitive user…

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SeqMonk
Desktop

SeqMonk

A program to enable the visualisation and analysis of mapped sequence data.…

A program to enable the visualisation and analysis of mapped sequence data. SeqMonk was written for use with mapped next generation sequence data but can in theory be used for any dataset which can…

Anno-J
Web

Anno-J

A web application designed for visualizing deep sequencing data and other…

A web application designed for visualizing deep sequencing data and other genome annotation data. Anno-J is intended to run in modern W3C compliant browsers, and allows flexible configuration of…

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MaqView
Desktop

MaqView

A graphical read alignment viewer. MaqView is specifically designed for the Maq…

A graphical read alignment viewer. MaqView is specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is nothing fancy as…

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BACContigEditor
Desktop

BACContigEditor

A simple sequence alignment editing tool, written in Java. BACContigEditor is…

A simple sequence alignment editing tool, written in Java. BACContigEditor is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole…

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MapView
Desktop

MapView

An information-rich short reads alignment viewer with genetic detection…

An information-rich short reads alignment viewer with genetic detection capability for next-generation sequencing technologies. MapView supports a compact alignment view for both single-end and…

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