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Genome visualization software tools | High-throughput sequencing data analysis

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data.

Source text:
(Barrios and Prieto, 2017) D3GB: An Interactive Genome Browser for R, Python, and WordPress. J Comput Biol.

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IGV / Integrative Genomics Viewer
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Enables users to explore large, integrated genomic datasets. IGV provides next-generation sequencing (NGS) data visualization and provides features for identification of sequencing and analysis artifacts, leading to errant single-nucleotide variant (SNV) calls, as well as support for viewing large-scale structural variants (SV) detected by paired-end read technology. The software also includes features to support third-generation long-read sequencing technologies. Several IGV features have been developed to aid manual review of aligned reads.
GenPlay
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Provides an analyser and browser tool for data expressed in multiple genomic coordinate systems. GenPlay can display RNA-seq, ChIP-seq, Methyl-seq, TimEX-seq and a variety of DNA sequence and annotation tracks. This software can used also for the evaluation of data aligned on custom genomes and offers a library of operations to process raw data. It enables data export into any of the coordinate systems that makeup the meta-reference genome.
Artemis
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Furnishes methodology for analyzing and displaying high-throughput sequence-based experimental data. Artemis is a tool that can be applied for annotate bacterial e.g. Salmonella enterica, Burkholderia cenocepacia and small and medium-sized eukaryote genomes e.g. Schistosoma mansoni. Moreover, this tool aims to analyze, browse and interpret large datasets being produced by high-throughput sequencing (HTS) experiments.
TnT / Trees and Tracks
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Consists of a set of libraries aimed at creating configurable and interactive re-usable visualizations of trees and track-based annotations. TnT is able to generate tree- and track-based visualizations for the web. The platform also provides an API that allows the development of many different visualizations ranging from simple species trees to complex visualizations comprising per-node data annotations.
Epiviz
An interactive visualization tool for functional genomics data. Epiviz supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. Epiviz sets a precedent for genomic data analysis collaborative workflows by enabling reproducible and shareable steps, and allowing custom user code to be dynamically incorporated, while guaranteeing the security and integrity of user data.
UCSC Xena
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Performs secure analyses and visualization of users’ private functional genomics data set in the context of public and shared genomic/phenotypic data sets. UCSC Xena is a Functional Genomics Browser that provides analytics, visualization and Galaxy integration for analyzing and viewing the public data hubs. It gives access to public databases (Xena Public Data Hubs) and allows users to mix in and compare private data (Xena Private Data Hubs).
Apollo
A browser-based genome editor that supports geographically dispersed researchers whose work is coordinated through automatic synchronization. The overall platform is currently comprised of a visualization component - JBrowse, and an editing and user authentication component - Apollo. With Web Apollo the task of manual curation is spread out among many hands and eyes, enabling the creation of virtual research networks of researchers linked by a common interest in a particular organism or population.
Savant
Enables visualization and navigation of reference genomes and corresponding genomic data sets. Savant is a genome browser that supports a wide range of file formats, as well as the use of remote files and datasources. Navigation to genomic regions of interest is assisted through textual search and bookmarks. The software delivers creative visualization representations for high-throughput sequencing (HTS) data and a plugin architecture that provides the opportunity to incorporate any computational tool within a visual environment.
GenomeView
Browses sequences, annotations, multiple sequence alignments and next-generation sequencing (NGS) data all at once and on a genome-wide scale. GenomeView can handle a broad range of the sequence data types resulting from NGS. The software provides uses with an overview of the data and can also to zoom-in down to a single nucleotide using semantic zooming. It offers a way to present the results and data to the scientific community for any genomics or sequence analysis project.
PGB / Personal Genome Browser
Provides comprehensive functional annotation and visualization for individual genomes based on the genetic-molecular-phenotypic model. Investigators can easily view individual genetic variants, such as single nucleotide variants (SNVs), INDELs and structural variations (SVs), as well as genomic features and phenotypes associated to the individual genetic variants. The PGB especially highlights potential functional variants using the PGB built-in method or SIFT/PolyPhen2 scores.
PopHuman
Provides description and analysis of comprehensive human diversity data. PopHuman is a population genomics-oriented genome browser. It represents an update to the 1000GP Phase III (2504 individuals, 26 populations, 84.7 million SNPs), but also dramatic improvements in the amount of data analyzed and browser performance. It also calculates species divergence, which allows the implementation of statistical tests to detect the signature of recurrent natural selection acting over prolonged periods of time.
Map Viewer
Provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. The number and types of available maps vary by organism, and are described in the "data and search tips" file for each organism. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.
GenomeGraphs
Facilitates analysis and visualization of mRNA-Seq data. GenomeGraphs is a visualization tool that allows complex customization to facilitate a more complete integration and representation of genomic datasets. The software relies on biomaRt package to retrieve genomic annotation information on-line from Ensembl using BioMart web services. GenomeGraphs can plot together several types of data using the same genome coordinate system. It also allows users to create custom annotation tracks.
myGenomeBrowser
Provides biologists with a way to build, query and share their genome browsers. myGenomeBrowser is a web-based designed to give users more autonomy while simplifying and minimizing intervention from system administrators. Its environment is based on JBrowse and supplemented with various features that are missing from current solutions, such as management of various data sources, mining tools and sharing systems. myGenomeBrowser is provided with an installation script based on the Docker container management system.
DiProGB / Dinucleotide Properties Genome Browser
An easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph.
GenomePlot
Displays a wide variety of data on a single genomic backbone in either a circular or linear format. GenomePlot is a visualization tool that allows users to zoom to the desired view of the data and to print or save the image to a file for producing publication quality illustrations. The software has been used to generate displays for several genomes, including Methanobacterium thermoautotrophicum, Helicobacter pylori, Clostridium acetolbutylicum, and Agrobacterium tumefaciens.
GenVisR
Provides a user-friendly, flexible, and comprehensive suite of tools for visualizing complex genomic data in three categories (small variant, copy number alteration, and data quality). By leveraging the abilities of ggplot2 it confers a level of customizability not previously possible. Virtually any aspect of a plot can be changed simply by adding an additional layer onto the graphical object. Thus, GenVisR allows for publication quality figures with a minimal amount of required input and data manipulation while maintaining a high degree of flexibility and customizability.
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