cFinder

cFinder detects, quantifies, and characterizes haplotypes in mixed samples using next-generation sequencing (NGS) data.

Key Features:

• Haplotype Detection and Quantification: Automatically identifies multiple haplotypes in mixed sequencing samples and quantifies their relative abundance.
• Variant Connection Reporting: Reports variant combinations forming haplotypes together with read counts and relative occurrence percentages.
• Paired-End Read Utilization: Incorporates paired-end sequencing information to improve haplotype detection accuracy.
• NGS Platform Compatibility: Supports analysis of sequencing data generated by multiple next-generation sequencing technologies and alignment strategies.
• Simulation-Based Validation: Demonstrates accuracy in haplotype detection through validation with simulated reads generated using GemSIM.

Scientific Applications:

• Cancer Mutation Analysis: Identifies clonal variants and compound mutations in genes such as BCR-ABL1 for resistance testing in oncology.
• Pathogen Population Analysis: Characterizes mixed viral, bacterial, or fungal populations in sequencing samples.

Methodology:

cFinder analyzes next-generation sequencing reads, including paired-end data, to detect linked variants forming haplotypes and quantifies their abundance within mixed samples.