Genomics Viewer

View NGS sequences and annotations

Description

The Genomics Viewer app lets you view and explore integrated genomic data with an embedded version of the Integrative Genomics Viewer (IGV) [1][2]. The genomic data include NGS read alignments, genome variants, and segmented copy number data.

Using the app, you can:

Visualize short-read data (.BAM or .CRAM) aligned to a reference sequence and compare multiple data sets aligned to a common reference sequence.
View coverage of different regions of the reference sequence.
Investigate quality and other details of aligned reads.
Display nonquantitative genome annotations (.BED, .GFF, .GFF3, and .GTF).
Load structural variants (.VCF) and visualize genetic alterations, such as insertions and deletions.
View segmented copy number data (.SEG) and quantitative genomic data (.WIG, .BIGWIG, and .BEDGRAPH), such as ChIP peaks and alignment coverage.

Open the Genomics Viewer App

MATLAB^® Toolstrip: On the Apps tab, under Computational Biology, click the app icon.
MATLAB command prompt: Enter genomicsViewer.

Examples

Visualize NGS Data Using Genomics Viewer App

Programmatic Use

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`genomicsViewer`

genomicsViewer opens a new instance of the Genomics Viewer app.

`genomicsViewer(Name=Value)`

genomicsViewer(Name=Value) uses one or more optional name-value arguments to add a reference genome, alignment, and other genomic data files as tracks in the app. For a list of name-value arguments, see genomicsViewer.

References

[1] Robinson, J., H. Thorvaldsdóttir, W. Winckler, M. Guttman, E. Lander, G. Getz, J. Mesirov. 2011. Integrative Genomics Viewer. Nature Biotechnology. 29:24–26.

[2] Thorvaldsdóttir, H., J. Robinson, J. Mesirov. 2013. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Briefings in Bioinformatics. 14:178–192.

Version History

Introduced in R2019b

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R2024a: `genomicViewer` opens new app instance

The genomicsViewer function now opens a new instance of the app. Previously, it changed the focus to the currently open app.

R2024a: Internet connection is no longer needed

The app no longer requires an internet connection to open. If you call genomicsViewer without specifying any reference sequence, the app uses Human (GRCh38/hg38) as the reference sequence by default. If you are offline, you must specify a local file to use as the reference. You can do so by specifying it as a name-value argument at the command line or by selecting Import Reference from the app.