IGV pipeline

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

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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 IN pipelines

 (220)
2018
PMCID: 5752202
PMID: 29297465
DOI: 10.7554/eLife.31216.024

[…] the scaling factor was calculated as a ratio of the number of alignments for each snp-parsed file relative to the file with the smallest number of alignments. h3k27me2/3 profiles were displayed in igv (thorvaldsdóttir et al., 2013) to examine the individual h3k27me2/3 profiles for wild-type and rearranged chromosome segments., all chip-seq and rna-seq data, as well as whole genome sequence […]

2018
PMCID: 5777819
PMID: 29309033
DOI: 10.7554/eLife.33292.023

[…] of 100 variants reduced noise associated with sampling error of any given variant., all 17 suppressor strains mapped in this manner displayed linkage to two loci. visual inspection of reads (in igv [robinson et al., 2011]) revealed single nucleotide variants within one gene at each locus for 16 of the strains. a last variant (in pd4148) was found by a single read spanning a 476 bp deletion, […]

2018
PMCID: 5785540
PMID: 29371665
DOI: 10.1038/s41467-017-02740-5

[…] peaks47, and all peaks with false discovery rate <1% were included. the uniquely mapping locations were used to generate the genome-wide intensity profiles, which were visualized using the igv genome browser48. promoter region was defined as ±2000 bp from the transcription start site. data are available online in the geo database (gse98134). for chip-qpcr experiments, cells were fixed […]

2018
PMCID: 5797788
PMID: 29445324
DOI: 10.3389/fnmol.2017.00435

[…] sequence or the arc locus (chr15:74,669,000–74,682,000), the paired sequences, i.e., along with its counterpart, were extracted to prepare a bam file. using samtools 1.2 (li et al., 2009) and integrative genomics viewer 2.3.66 (robinson et al., 2011), we found many of the counterpart reads were mapped to a region around chr12:78,138,000. then, read pairs in which at least one of mates […]

2018
PMCID: 5814564
PMID: 29449667
DOI: 10.1038/s41598-018-21514-7

[…] sequences were predicted by the g4hunter program17, with default settings. the mapped reads per window, fold-change of mapped reads, and locations of predicted g4 quadruplex sites were visualised in.igv format on the integrative genome viewer44 and on the uscs genome browser45., , electronic supplementary material , supplementary information accompanies this paper […]

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).