NGSCheckMate

NGSCheckMate verifies sample identity across next-generation sequencing datasets by comparing allele read fractions at known single-nucleotide polymorphisms to confirm matching datasets from the same subject.

Key Features:

• Versatility Across Data Types: Handles exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing, and single-cell whole-genome sequencing.
• Model-based Genotype Comparison: Compares allele read fractions at known SNPs using a model-based method for genotype similarity assessment.
• Depth-dependent Similarity Metrics: Accounts for the depth-dependent behavior of similarity metrics when comparing datasets.
• Minimal Sequencing Depth Requirement: Operates effectively at sequencing depths greater than 0.5X.
• Alignment-free Module: Provides an alignment-free analysis that can be run directly on FASTQ files for rapid checks.
• File Format Support: Accepts FASTQ, BAM, and VCF files for sample identity verification.

Scientific Applications:

• Quality Control in NGS studies: Serves as a QC step to verify that datasets are correctly paired to subjects across NGS experiments.
• Sample Identity Verification: Detects mismatched or swapped samples across multi-modal or multi-sample datasets.
• Large-scale Genomic Projects: Applies to cohort studies, clinical trials, and population genetics projects where multiple samples or data types are profiled per subject.

Methodology:

Compares allele read fractions at known SNPs using a model-based method that accounts for sequencing-depth-dependent behavior, and includes an alignment-free module that analyzes FASTQ files directly.