Scalpel

Scalpel detects insertions and deletions (INDELs) in next-generation sequencing exome-capture data to enable sensitive and specific discovery of indel mutations.

Key Features:

• Integration of Mapping and Assembly: Combines mapping and local assembly to improve identification of INDELs in complex genomic regions.
• Repeat Analysis and Self-Tuning K-mer Strategy: Performs detailed repeat analysis and applies a self-tuning k-mer strategy to enhance detection within near-perfect repeats.
• Exome-capture Optimization: Tailored for exome-capture data from next-generation sequencing workflows.
• Sensitivity and Specificity: Optimized to achieve high sensitivity and specificity in indel discovery.
• Performance Superiority: Reported to outperform other state-of-the-art indel discovery approaches, particularly in repetitive genomic landscapes.

Scientific Applications:

• Inherited and De novo Mutation Discovery: Detection of inherited and de novo INDELs in genetic research studies.
• Simons Simplex Collection Analysis: Applied to analysis of 593 families from the Simons Simplex Collection to identify long (≥30 bp) transmitted INDELs.
• Autism Genetics: Used to detect enrichment of de novo likely gene-disrupting indels in autistic children.

Methodology:

Combines mapping and local assembly with detailed repeat analysis and a self-tuning k-mer strategy; the self-tuning k-mer dynamically adjusts k-mer selection based on repeat analysis to optimize INDEL detection accuracy.