ngsCAT

ngsCAT evaluates enrichment performance of targeted sequencing by analyzing mapped reads against predefined targeted regions to quantify coverage uniformity and enrichment specificity for loci or exomes in the human genome.

Key Features:

• Input Flexibility: Accepts input files containing mapped reads and coordinates of targeted regions, enabling assessment of specific loci or entire exomes within the human genome.
• Comprehensive Metrics: Generates detailed reports comprising multiple metrics and visualizations to evaluate the efficiency of the enrichment process.
• Comparative Analysis: Performs pairwise comparisons between two samples to assess variations between experiments or conditions.
• Quality Control: Quantifies sensitivity and specificity of the enrichment process to support quality control in NGS workflows.

Scientific Applications:

• Targeted Sequencing Projects: Evaluates capture efficiency and bias in targeted sequencing experiments.
• Exome and Locus Studies: Assesses enrichment performance for exome sequencing or specific loci where precise capture is required.
• Experimental Comparisons: Compares enrichment outcomes across experimental setups or conditions to evaluate consistency and reliability.

Methodology:

Analyzes mapped read data against predefined targeted regions and computes metrics such as coverage uniformity and enrichment specificity, with support for single-sample assessment and pairwise sample comparisons.