SmMIP-tools

SmMIP-tools processes and analyzes single-molecule molecular inversion probe (smMIP) sequencing data to enable high-multiplex targeted next-generation sequencing (NGS) experiments and sensitive detection of genetic variants.

Key Features:

• Integrated analytic pipeline: Consolidates quality control, read–smMIP linkage generation, molecular tag retrieval, and variant calling into a single computational pipeline.
• Read processing tool: Performs quality control, establishes linkages between sequencing reads and smMIPs, and retrieves molecular tags.
• Error-aware variant caller: Detects single nucleotide variants (SNVs) and short insertions and deletions (indels) while accounting for sequencing errors to improve accuracy.
• Benchmarking and validation: Validated on a cell-line DNA dilution series and a cohort of blood cancer patients with results concordant with clinical sequencing reports.

Scientific Applications:

• High-multiplex targeted NGS studies: Enables smMIP-based high-multiplex targeted NGS experiments for genetic research.
• Personalized medicine: Supports sensitive detection of genetic variants in contexts relevant to personalized medicine.
• Clinical research in hematologic malignancies: Applied to analysis of blood cancer patient cohorts with demonstrated concordance to clinical sequencing reports.
• Assay development and validation: Used for analytical validation workflows such as cell-line DNA dilution series.

Methodology:

Performs quality control, generates read–smMIP linkages, retrieves molecular tags, and applies an error-aware variant caller to detect SNVs and short indels.