Straglr

Straglr performs genome-wide scans and targeted genotyping of tandem repeat (TR) expansions using long-read alignments to characterize TR expansions implicated in over 40 neurological disorders.

Key Features:

• Genome-wide TR expansion scanning: Performs genome-wide scans to identify tandem repeat (TR) expansions across the genome.
• Targeted genotyping: Genotypes specific, known TR loci for detection of disease-associated expansions.
• Novel expansion detection: Detects previously unidentified TR expansions for discovery of potential pathogenic variants.
• Long-read alignments: Leverages long-read sequencing alignments to improve resolution and accuracy of TR expansion detection.
• Benchmarking and validation: Validated through benchmarking with simulations, targeted genotyping data from cell lines with known disease-associated expansions, and whole-genome sequencing with chromosome-scale assembly.

Scientific Applications:

• Diagnostic genotyping: Targeted genotyping of known pathogenic TR expansions to support genetic studies of neurological disorders.
• Discovery of novel TR expansions: Genome-wide identification of previously uncharacterized TR expansions that may be implicated in disease.
• Method benchmarking: Development and evaluation of TR detection methods using simulations and cell-line datasets with known expansions.
• Assembly-scale analysis: Characterization of TR expansions in whole-genome sequencing data and chromosome-scale assemblies.

Methodology:

Performs genome-wide scans and targeted genotyping using long-read sequence alignments; benchmarking was conducted with simulations, targeted genotyping data from cell lines bearing known disease-associated expansions, and whole-genome sequencing with chromosome-scale assembly.