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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.

The app requires an internet connection.

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.

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.

Introduced in R2019b