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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.
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 accelerate the translation of genomic data into new biological insights, therapies, and clinical trials. OncoPrinter takes a mutation data file and outputs genetic alteration like Amplification, Deep Deletion, mRNA Upregulation, mRNA Downregulation, Fusion, Truncating Mutation, Inframe Mutation, and Missense Mutation.
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Assists users to organize and centralize all variant data and annotations from their lab. Highlander provides researchers several tools for filtering information. This tool, coupled to a local MySQL database, aims to classify all variant data coming from exome- and whole genome sequencing experiments. It also supplies annotations or visualizations functions that allow to detect changes-of-interest amongst the complete list of variants detected in a sample.
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 the GENESIS (formerly GEM.app) platform are: 1) to assist scientists/clinicians in transferring and processing genomic data, 2) to produce accurate, high quality, and reproducible results, 3) to provide a highly available and scalable analytical framework for analyzing variant data, and 4) to provide tools for user-driven data-sharing and collaboration. Hereby, GENESIS enables users of varying computational experience to iteratively test many different filtering strategies in a matter of seconds and to browse very large sets of full exomes and genomes in real-time.
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.
Saccharomyces Genome Database Variant Viewer
Allows to explore and highlight differences in DNA and protein sequences. Saccharomyces Genome Database Variant Viewer displays similarity scores and sequence variants for open reading frames (ORFs) within a reference panel of Saccharomyces cerevisiae genomes. The software can to simultaneously visualize high-level differences of many genes, as well as sequence changes in individual features. It can also be repurposed for use on other websites.
BPS / BreakPoint Surveyor
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 supporting analysis from individual samples on a laptop to very large data sets on compute clusters. Its rendering engine is coupled with a flexible pipeline to detect structural variants, and it accommodates a variety of toolsets and analyses of whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) data.
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 programmers. Developers need to write code around BioCircos.js to build web applications. BioCircos.js provides flexible and powerful functionality for the development of web-based circular visualization tools for multi-faceted biological data. These applications will be developed as plugins to simplify the process of generating circular image.
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 user-specified regions (e.g. chromosome) may be inputted and viewed, with variant genotypes being colour coded. The variants displayed and their number will change depending on the quality and read depth filtering selected, allowing users to assess the robustness of the data and analysis.
SVPV / Structural Variant Prediction Viewer
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 annotation of population allele frequencies from reference SV datasets. Gene annotations may also be included. The application is capable of running in a graphical user interface (GUI) mode for visualising SVs one by one, or in batch mode for processing many SVs serially. SVPV supports variant call format (VCF) structural variant types deletion (DEL), duplication (DUP), copy number variation (CNV), inversion (INV), insertion (INS) and breakend ('BND'). Delly2-style translocations (TRA) are also supported.
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 about exact chromosomal position, zygosity and frequency, with point-and-click information regarding dbSNP IDs, gene association and variant inheritance. Rare variants as well as de novo variants can be flagged in different colors. The various RareVariantVis functions are also applicable in somatic alterations, for example in analysis of cancer genomes, where information about zygosity is essential.
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 visual analytics concepts to assist users. It was developed in the framework of the Malaria Genomic Epidemiology Network (MalariaGEN), a worldwide community of researchers studying the biology and epidemiology of malaria through the collection and analysis of genome variation data of human, parasite and mosquito populations.
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 phylogeography, allele frequency map and principal coordinate analysis. SVAMP takes VCF files (variant call format) as input. Metainformation on samples are simple tab delimited text files. In addition SVAMP also reads annotation files in GFF format and reference sequences in FASTA format.
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.
Facilitates personal genome annotation and interpretation. SeqsLa is a genomic analysis platform that provides (i) lightning-fast annotation workflow, (ii) comprehensive structural variant annotation, (iii) user-friendly graphical interface, and (iv) others variant filtering utilities. It also includes seven types of filters, which are general property, medical relevance, variant effect, splicing event, genome position, quality control, and tissue specificity, to fulfill different aspects of filtering strategies.
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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 interactive and animated features. This tool complements existing cancer genome portals by providing a comprehensive and intuitive view of pediatric cancer genomic data with advanced visualization features, as well as integration of expression and adult cancer data.
VCS / Visualization of CNV or SNP
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 genome contents in region having specific range like: gene, long interspersed nuclear element [LINE], short interspersed nuclear element [SINE], long terminal repeat [LTR], simple repeat, low complexity, miRNA, tRNA, CpG island, and Gene Ontology - Biological Process, Molecular Function, and Cellular Component.
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