Integrative Genomics Viewer (IGV): High-performance Genomics Data Visualization and Exploration

Overview

Journal Brief Bioinform

Publisher Oxford University Press

Specialty Biology

Date 2012 Apr 21

PMID 22517427

Citations 4599

Authors

Helga Thorvaldsdottir

James T Robinson

Jill P Mesirov

Affiliations

Soon will be listed here.

Abstract

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.

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References

Kent W, Zweig A, Barber G, Hinrichs A, Karolchik D . BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010; 26(17):2204-7. PMC: 2922891. DOI: 10.1093/bioinformatics/btq351. View

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

Carver T, Bohme U, Otto T, Parkhill J, Berriman M . BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics. 2010; 26(5):676-7. PMC: 2828118. DOI: 10.1093/bioinformatics/btq010. View

Beroukhim R, Mermel C, Porter D, Wei G, Raychaudhuri S, Donovan J . The landscape of somatic copy-number alteration across human cancers. Nature. 2010; 463(7283):899-905. PMC: 2826709. DOI: 10.1038/nature08822. View

Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F . Tablet--next generation sequence assembly visualization. Bioinformatics. 2009; 26(3):401-2. PMC: 2815658. DOI: 10.1093/bioinformatics/btp666. View

Li H . Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011; 27(5):718-9. PMC: 3042176. DOI: 10.1093/bioinformatics/btq671. View

Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M . The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156-8. PMC: 3137218. DOI: 10.1093/bioinformatics/btr330. View

Berman B, Weisenberger D, Aman J, Hinoue T, Ramjan Z, Liu Y . Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2011; 44(1):40-6. PMC: 4309644. DOI: 10.1038/ng.969. View

Robinson J, Thorvaldsdottir H, Winckler W, Guttman M, Lander E, Getz G . Integrative genomics viewer. Nat Biotechnol. 2011; 29(1):24-6. PMC: 3346182. DOI: 10.1038/nbt.1754. View

10.

. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455(7216):1061-8. PMC: 2671642. DOI: 10.1038/nature07385. View

11.

Guttman M, Amit I, Garber M, French C, Lin M, Feldser D . Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009; 458(7235):223-7. PMC: 2754849. DOI: 10.1038/nature07672. View

12.

. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004; 306(5696):636-40. DOI: 10.1126/science.1105136. View

13.

Fiume M, Williams V, Brook A, Brudno M . Savant: genome browser for high-throughput sequencing data. Bioinformatics. 2010; 26(16):1938-44. PMC: 3271355. DOI: 10.1093/bioinformatics/btq332. View

14.

Dowell R, Jokerst R, Day A, Eddy S, Stein L . The distributed annotation system. BMC Bioinformatics. 2001; 2:7. PMC: 58584. DOI: 10.1186/1471-2105-2-7. View

15.

Verhaak R, Hoadley K, Purdom E, Wang V, Qi Y, Wilkerson M . Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010; 17(1):98-110. PMC: 2818769. DOI: 10.1016/j.ccr.2009.12.020. View

16.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

17.

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M . Artemis: sequence visualization and annotation. Bioinformatics. 2000; 16(10):944-5. DOI: 10.1093/bioinformatics/16.10.944. View