TEQC

TEQC assesses and visualizes quality metrics for target enrichment (hybridization-based capture) experiments and per-target read coverage in exome and other high-throughput sequencing studies.

Key Features:

• Quality Measures: Provides comprehensive quality metrics including specificity and sensitivity of the capture process.
• Enrichment Analysis: Evaluates enrichment efficiency for targeted regions.
• Per-target Read Coverage: Computes read coverage on a per-target basis from sequencing data.
• Probe Characteristics Correlation: Analyzes correlations between hybridization probe characteristics and read coverage.
• Coverage Uniformity and Reproducibility: Assesses coverage uniformity across targets and evaluates reproducibility between experiments.
• Read Duplicate Analysis: Analyzes read duplicates to identify biases introduced by PCR amplification.
• Diagnostic Plots: Generates diagnostic plots for visual inspection of data quality and quality metrics.

Scientific Applications:

• Exome Sequencing: Supports quality assessment of exome sequencing datasets generated by hybridization-based target capture.
• Cancer Genomics: Provides targeted sequencing quality control for cancer genomics studies.
• Genetic Variation Analysis: Enables assessment of input-data quality for studies of genetic variation.
• Variant Calling: Improves readiness of target-enriched datasets for variant calling pipelines.
• Gene Expression Profiling: Ensures coverage quality for gene expression analyses of captured regions.
• Comparative Genomics: Supports comparative analyses by evaluating consistent target coverage across samples.

Methodology:

Generates diagnostic plots for visual inspection of target enrichment quality metrics and is implemented as an R/Bioconductor package (requires R > 2.12.0).