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Genomics Viewer

View NGS sequences and annotations

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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.

Genomics Viewer app

Open the Genomics Viewer App

  • MATLAB® Toolstrip: On the Apps tab, under Computational Biology, click the app icon.

  • MATLAB command prompt: Enter genomicsViewer.

Examples

Programmatic Use

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genomicsViewer opens a new instance of the Genomics Viewer app.

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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See Also

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