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.
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.
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.
Allows users to directly process and analyze next-generation sequencing data. GENESIS is a web platform that ensures the discovery of phenotypic overlaps, very rare disease gene variants, and global matchmaking based on patient phenotype/ genotype data. This server can assist scientists in transferring and processing genomic data. It also produces reproducible results.
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.
Allows visualization of genomic rearrangements. CouGaR-viz is a visualization package that can illustrate the results of CouGaR in an interpretable format. The software lays out complex genomic rearrangements, specifically focusing on those occurring in amplified regions. It uses a gene annotation file to compare the coordinates of rearrangements to the gene annotations.
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 Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features.
Detects and allows interactive visualization of single-nucleotide polymorphisms (SNPs). QualitySNPng combines SNP detection and genotyping with interactive visualization of the results. This software provides a graphical user interface with pre-set filter options that is configurable for specific needs. It is appropriate to use in marker SNP identification or to analyze RNA-seq data with up to several million reads per transcript to genotype a mixture of a hundred accessions.
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.
A tool to visualize read-depth and pair-end information as it originally comes from NGS machines at various resolutions. Its main purpose is to provide intuitive visualizations for an easier exploration or detections of structural variations. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference.
Permits the exploration of patterns among tumor samples arranged relative to one another based on their molecular similarities. TumorMap consists of an analysis and visualization web portal that presents samples on the basis of their molecular profile similarity and attributes associated with samples, such as disease histological subtypes. Furthermore, this platform allows users to build their own interactive maps from several uploaded high-throughput platforms.
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.
A web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales.
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.
Allows visualization of structural variants (SVs), sorting and displaying only reads relevant to a candidate SV. svviz can serve to display arbitrary SV types such as translocations, deletions and insertions, inversions and mobile-element insertions. It can be used to summarize statistics and PDF or SVG visualizations for hundreds or thousands of SVs with a single command. This tool supports data from most modern sequencing platforms.
Investigates genome sequence data (including non-coding regions) for both germ line and somatic variants. RareVariantVis displays 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. The tool’s functions can be applied 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.