IGV statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IGV
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Tool usage distribution map

This map represents all the scientific publications referring to IGV per scientific context
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Associated diseases

This word cloud represents IGV usage per disease context
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Popular tool citations

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Protocols

IGV specifications

Information


Unique identifier OMICS_00917
Name IGV
Alternative names Integrative Genomics Viewer, IGVtools, Integrated Genome Viewer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 3.0, MIT License
Computer skills Medium
Version 2.4.8
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline James Robinson
  • person_outline IGV Team

Additional information


http://software.broadinstitute.org/software/igv/UserGuide

Publications for Integrative Genomics Viewer

IGV citations

 (1623)
library_books

Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment

2018
Nat Commun
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w

[…] Agilent Technologies). Libraries were sequenced on a MiSeq or HiSeq2000 (Illumina). Mapping and variant call were performed using SureCall v2.1.0.21. Variants in ITSN2 were manually verified using an Integrative Genomics Viewer (IGV), and nonsynonymous mutations were retained and filtered for a MAF < 0.01 in the 1000 Genomes database and HGVD. […]

call_split

Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

2018
Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y
call_split See protocol

[…] all box plots, the boxes extend between the 25th and 75th percentiles, the center line shows the median, and the whiskers represent the minimal and maximal values. ChIP-seq tracks were created using Integrative Genomics Viewer (http://software.broadinstitute.org/software/igv/). […]

call_split

Systematic pan cancer analysis of somatic allele frequency

2018
Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0
call_split See protocol

[…] reads counts for all the variant positions in all four datasets (normal exome, normal transcriptome, tumor exome and tumor transcriptome). Selected read count assessments were visually examined using Integrative Genomics Viewer. We excluded from further analyses variants which (1) were covered with less than 10 sequencing reads in the tumor DNA or the RNA sequencing data; (2) reside in known impri […]

library_books

Outlier response to anti PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors

2018
Nat Commun
PMCID: 5951831
PMID: 29760383
DOI: 10.1038/s41467-018-04322-5

[…] D) and/or an AD/DP ratio of <0.05 and/or a population frequency higher than 1% (popfreq_all >0.01) were filtered out. All somatic mutations called by this procedure were controlled manually using the Integrative Genomics Viewer (IGV).Sashimi plots were generated with the R software version 3.4.2 and its packages GenomicAlignments (1.12.2) and GenomicRanges (1.28.4) from data downloaded through the […]

call_split

Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human infecting blood fluke, Schistosoma mansoni

2018
Sci Rep
PMCID: 5943310
PMID: 29743617
DOI: 10.1038/s41598-018-25463-z
call_split See protocol

[…] enome. Mitogenomes based on the two methods were aligned and manually checked for consistency. To check read support consistency, reads were mapped to final assembled mitogenomes and visualized using Integrated Genome Viewer.Mitogenome annotation was done using MITOS2 that includes the latest protein identification model,. We used two references in MITOS2, RefSeq63 Metazoa and RefSeq81 Metazoa, to […]

call_split

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic 5

2018
PLoS One
PMCID: 5940187
PMID: 29738565
DOI: 10.1371/journal.pone.0196965
call_split See protocol

[…] eaks and create the MA plots. Venn diagrams overlapping the different sets of peaks were created using ChIPpeakAnno []. Both DiffBind and ChIPpeakAnno are packages available on Bioconductor [, ]. The Integrative Genomics Viewer was used to visualize the ChIP-seq data []. Motif analysis was performed using Hypergeometric Optimization of Motif EnRichment (HOMER) with a 1 kb window centered at the GB […]


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IGV institution(s)
School of Medicine, University of California San Diego, La Jolla, CA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Pacific Biosciences, Menlo Park, CA, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
IGV funding source(s)
Supported by the NCI (NIH/NCI) grants R01CA157304 and U24CA210004 and the Starr Cancer Consortium grant I5-A500.

IGV reviews

 (2)
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Gyan Prakash Mishra

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Desktop
IGV is the first choice for quick visualisation of NGS data. It takes BAM file (along with .bai file), .bedGraph file, .bigWig.

Fabien Pichon

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Desktop
A simple viewer. You can not do a lot with it, but you can visualize your mapping and that's its job !
To me, it miss however the possibility to add landmarks (vertical lines).