Genome viewer 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.
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.
Allows visualization and sharing of next-generation sequencing (NGS) data. GBrowse is a web-based genome browser divided between code that runs on the web server and on the web browser client. The software is suitable for installation on public web sites, as well as the web sites of small-to medium collaborations among several geographically separate groups. It also integrates well with the other bioinformatics tools in the Generic Model Organism Database (GMOD) suite.
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.
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.
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
Supplies tools for the analysis and visualization of genomic data. JMP Genomics offers features for genomic selection for crop improvement, pharmacogenomics, expression, statistical genetics, next-gen sequencing, linkage mapping as well as predictive modeling. The software allows the analysis of rare and common variants, detection of differential expression patterns, identification of signals in next-generation sequencing data, discovery of reliable biomarker profiles, and visualization of patterns.
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.