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 (
.BAMor.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.
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.