Variant Review with the Integrative Genomics Viewer Robinson, James T; Thorvaldsdóttir, Helga; Wenger, Aaron M ...
Cancer research (Chicago, Ill.),
2017-Nov-01, 2017-11-01, 20171101, Letnik:
77, Številka:
21
Journal Article
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Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection ...can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and interpretation of NGS datasets, as well as other types of genomic data. Here, we present a short overview of IGV's variant review features for both single-nucleotide variants and structural variants, with examples from both cancer and germline datasets. IGV is freely available at https://www.igv.org
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Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database ...(MSigDB) is one of the most widely used repositories of such sets.
We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.
MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.
Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major ...challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.
The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown ...beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of “hallmark” gene sets as part of MSigDB. Each hallmark in this collection consists of a “refined” gene set, derived from multiple “founder” sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.
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•We generate 50 “hallmark” gene sets from the Molecular Signature Database (MSigDB)•This required a hybrid approach combining computation with manual expert curation•The hallmarks reduce redundancy and produce more robust enrichment analysis results•We plan to move forward with a program to enhance and expand the hallmarks collection
Through extensive automated and manual curation, Liberzon et al. provide a refined and concise collection of “hallmark” gene sets from the Molecular Signatures Database for gene set enrichment analysis.
Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most ...alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples.
To help address this problem, we present Sashimi plots, a quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad Integrated Genome Viewer or with a stand-alone command line program.
Software code and documentation freely available here: http://miso.readthedocs.org/en/fastmiso/sashimi.html
Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox ...application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code.
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•Juicebox.js enables users to explore Hi-C contact maps from their web browser•The exact state of the browser can be encoded in a sharable URL•Users can create sharable maps of their own data in a few minutes
Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring and sharing the resulting datasets. Users can create sharable visualizations of their own datasets in a few minutes using cloud storage providers such as Dropbox, Google, and Amazon without coding.
Interactive analysis notebook environments promise to streamline genomics research through interleaving text, multimedia, and executable code into unified, sharable, reproducible “research ...narratives.” However, current notebook systems require programming knowledge, limiting their wider adoption by the research community. We have developed the GenePattern Notebook environment (http://www.genepattern-notebook.org), to our knowledge the first system to integrate the dynamic capabilities of notebook systems with an investigator-focused, easy-to-use interface that provides access to hundreds of genomic tools without the need to write code.
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•We integrated the GenePattern genomics platform with the Jupyter Notebook environment•Notebooks interleave text, graphics, and analyses into complete “research narratives”•Users can embed genomic analyses into notebooks without the need to write code•GenePattern Notebook is freely available at http://www.genepattern-notebook.org
Reich et al. have developed software that integrates the capabilities of electronic analysis notebooks and bioinformatics analysis portals. GenePattern Notebook uses the popular Jupyter Notebook platform that interleaves text, graphics, and code, and brings these tools for reproducible research, as well as access to hundreds of bioinformatics analyses, to non-programmers.
Abstract
Summary
igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external ...dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required.
Availability and implementation
The igv.js JavaScript component can be installed from NPM at https://www.npmjs.com/package/igv. The source code is available at https://github.com/igvteam/igv.js under the MIT open-source license. IGV-Web, the end-user application built around igv.js, is available at https://igv.org/app. The source code is available at https://github.com/igvteam/igv-webapp under the MIT open-source license.
Supplementary information
Supplementary information is available at Bioinformatics online.
A genomic data viewer for iPad Thorvaldsdóttir, Helga; Robinson, James T; Turner, Douglass ...
Genome Biology,
02/2015, Letnik:
16, Številka:
1
Journal Article
Recenzirano
Odprti dostop
The Integrative Genomics Viewer (IGV) for iPad, based on the popular IGV application for desktop and laptop computers, supports researchers who wish to take advantage of the mobility of today's ...tablet computers to view genomic data and present findings to colleagues.
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