Structural Variation Detection
NextGENeLR provides fast and accurate
alignments of long sequencing reads
and enables accurate detection of
structural variants.
NextGENeLR uses a specialized long read alignment algorithm. This alignment algorithm works by first
indexing the reference sequence, compressing homopolymer regions, which allows homopolymer
length differences to be tolerated during alignment. A separate index table is saved for each
chromosome. Reads are also similarly indexed. Each chromosome table is then searched for matches.
The region with the most and longest matches is selected and a local alignment is performed. The long
reads can be split to properly align reads containing structural variants. For each read the alignment
positions for each section are compared to the reference. Any differences between the reads and
reference are evaluated to determine the structural variant type, as shown in Figure 1 below. If sections
of a read align to different chromosomes than a translocation is reported. If sections of a read align in
different directions, then an inversion is reported. Similar breakpoints, within 5bp, are merged.

Figure
1: NextGENeLR makes structural variant
calls by comparing the alignment positions
for the sample and the reference.
The patterns above illustrate how
the structural variant type is reported.
Once analysis is completed the generated BAM file can be viewed using NextGENeLR’s Alignment
Viewer. The Structural Variation Table is shown by default, with the Pileup Viewer above the table.
The Structural Variation Table lists the detected structural variants. For each variant, a type is provided
as well as the number of reads supporting the structural variant, the breakpoint positions, the frequency
of the variant out of the total reads aligned at each breakpoint position, and the distance in bp for the
sample and the reference.

Figure
2: NextGENeLR Alignment Viewer showing
the Structural Variation Table. Highlighted
is a 413bp deletion.
For more information Review
or Download Application notes:
Structural Variation Detection from Pacific Biosciences Data using NextGENe®LR
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