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.
Allows the data integration, data processing, and visualization. ZENBU is a web-based system that consists of: (1) an expression data enhanced genome browser interface, (2) a secured user system for data upload and data sharing and (3) a data explorer interface to find and manipulate data across many supported experimental data types and to find shared user configurations. It allows customization of data filters, views and analyses.
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.
Implements a suite of tools for genomic sequence data analysis using general variation graph references. vg allows users to construct or import a graph, modify it, visualize it, and use it as a reference. The software can map new sequence reads to the reference using succinct indexes of the graph and its sequence space, and can describe variation between a new sample and an arbitrary reference embedded as a path in the graph.
Allows users to run various analysis with PCAWG data. PCAWG-Scout authorizes studies as well as cancer driver genes prediction, recurrent structural variation, pathway enrichment or predictions of recommended therapies based on the resource PanDrugs. Users can access to an array of reports and visualizations to produce results in real-time, and discover trends as well as form and test hypotheses.
Consists of a visual analysis environment for next generation sequencing (NGS) data. Trackster is a tool that can be applied for studying selected data subsets rather than a complete dataset. It is designed to enable interactive, visual search of analysis settings and also to display and filter isoforms. Moreover, this application allows visualization of SAM/BAM, BED, GFF/GTF, WIG, bigWig, bigBed, bedGraph, and VCF datasets within Galaxy.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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.
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.
Allows visualization of functional genomics data. Epiviz supports genome navigation like other genome browsers, but permits multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It sets a precedent for genomic data analysis collaborative workflows by enabling reproducible and shareable steps, and users code can be incorporated, while guaranteeing the security and integrity of user data.
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.
Proposes a solution to display or interpret different types of data. JBrowse uses pre-generation of image tiles, data structures, and client-side rendering for offering an interactive browsing tool. This software provides functionalities allowing researchers to observe users-imported genomes in scrolling or zooming. This tool is available through a web application or as a desktop version.
Displays and permits exploration of genomic data and annotations for RNA-Seq and ChIP-Seq data sets. IGB attributes colors from a heatmap using quantitative variables associated with features, allows visual investigation. It can be used for dynamic manipulation of quantitative data via genome graphs. This tool supports real-time zooming and panning through a genome. It can increment or load genome-scale data from remote web servers or local files
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).
Enables tightly integrated comparative variant analysis and visualization of thousands of next generation sequencing (NGS) data samples and millions of variants. BasePlayer is a highly efficient and user-friendly software for biological discovery in large-scale NGS data. It transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries.
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.
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.
Provides an integrated view of omics datasets based on genomic coordinate axes. OmicBrowse is a genome browser that integrates multiple heterogeneous databases into a single omic space. The software employs a graphics interface that assists effective genome-wide analysis with various data records stored in multiple databases. It can be installed on a user’s PC and thus works as a user’s private databases.
Allows users to conduct common analyses of RNAseq and ChIPseq data. SeqBox can be useful for genomic mapping, experimental power evaluation, differential expression, or transcription factors/histone-marks peaks identification, for instance. This tool is composed of SeqBox software and SeqBox target hardware.
Allows users to compare pairs of bacterial genomes. BugView is a genome browser for viewing, comparing and annotating genes on related-primarily bacterial-genomes. It reads genomes in the GenBank file format in which most bacterial genome sequences are available, and with which biological scientists are familiar. It can also load eukaryotic chromosomes, display genes containing multiple exons, and ‘stagger’ the display of genes or transcripts with overlapping co-ordinates.
Permits users to visualize and explore genomics annotations and high-throughput data. ggbio provides applications to create both typical and non-typical biological plots for genomic data. This package supports both the convenient construction of typical genomic plots, while simultaneously supporting the invention of new types of plots from low-level building blocks.