Genome Browser | Strand NGS

Genome Browser

Overview

Genome Browser is a representation of a complete genome on which the sequenced reads can be visualized. Annotation data, such as cytobands, genes, and transcripts, can be superimposed, as well as results from various analyses, such as peak regions, SNPs, and gene fusions. Watch a recording of our Genome Browser webinar to learn more about its features.

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Elastic Genome Browser

The elastic genome browser can display multiple genomic regions simultaneously. Each genomic region can be viewed at a different zoom level allowing for uninteresting regions to be collapsed and interesting regions to be expanded. The elastic bookmark format allows specification of regions and zoom levels. Algorithms output bookmarks customized to each result region.

Semantic zooming

Genome Browser is equipped with semantic zooming, displaying visualizations based on the zoom level. At low zoom level, only the coverage line plot is shown. At intermediate zoom level, both the coverage and reads are shown, with colors indicating the mismatch bases. At high zoom level, all bases are displayed as colored letters.

Intermediate zoom level

Reads start to show up below the coverage plots. The reads are shown as colored bars. Gray indicates the reads match the reference sequence perfectly. Colors within the reads highlight mismatched bases.

Visualizing spliced reads

If reads are spliced (typically in RNA-Seq experiments), the read is shown split between the two (or more) positions, separated by a grey line. For paired-end reads, the two reads are separated by a black line.

Paired read visualization

For paired-end or mate-paired data, the mate status is indicated with colors. Reads with missing mates are colored in red, while mates that align far from each other are colored black. Clusters of reads of the same color help users verify structural variations predicted by the tool.

Mismatch coverage

A stacked histogram on the coverage plot shows locations with a large number of mismatches. Colors of the histogram represent the proportion of bases. The presence of the histogram indicates possible SNP locations.