STR Alignment Visualization

TruSight Software includes an embedded visualization of read alignments to a short tandem repeat (STR) locus, enabling inspection of the genotype predictions.

The generated image displays read alignments to a modified reference genome. The modified reference consists of the STR sequence that is long enough to accommodate alignments of all reads, and the sequence immediately flanking the repeat. Vertical lines delineate repeat sequences from flanking sequences and other repeat units.

The modified reference and aligned reads are sectioned vertically into consecutive STR and non-STR regions (graph nodes). All aligned reads from the sample are grouped horizontally into blocks, each block consisting of all reads with a unique STR count for the selected repeat unit. The top row of each block displays the sequence of modified reference, followed by the aligned sequences of reads with the corresponding STR count.

For more information, see https://github.com/Illumina/GraphAlignmentViewer.