REViewer

REViewer visualizes haplotype-resolved sequencing read alignments across tandem repeat regions to assess and interpret long repeat expansions.

Key Features:

• Haplotype Reconstruction: Reconstructs local haplotype sequences and aligns reads accounting for fragment lengths, coverage patterns, large insertions, and misalignments.
• Read Pileup Generation: Aligns reads to reconstructed haplotypes to generate read pileups that highlight repeat expansions and low-confidence genotype calls.
• Clinical Annotation: Compares visual assessments with triplet repeat primed PCR results and demonstrated high concordance with FMR1 repeat allele data.

Scientific Applications:

• Neurogenetic Disorder Analysis: Detects interruptions within repeat sequences and flanking regions and aids interpretation for conditions such as Huntington disease and familial amyotrophic lateral sclerosis.

Methodology:

Reconstructs haplotype sequences from sequencing data, distributing reads consistently with fragment lengths and coverage patterns to resolve repeat expansion ambiguities.