ngsReports

ngsReports provides R/Bioconductor functions to import, manage, visualize, and analyze next-generation sequencing (NGS) quality-control outputs such as FastQC and Picard to support QC in high-throughput studies.

Key Features:

• Integration with Popular QC Tools: Imports and manages outputs from FastQC and Picard within R/Bioconductor.
• Direct Import of NGS Reports: Supports reading FastQC reports and other NGS log files into R objects for analysis.
• Advanced Visualization: Produces customizable plots of QC metrics across numerous samples to summarize per-sample and aggregate metrics.
• Hierarchical Clustering: Performs hierarchical clustering on imported QC metrics to identify outlier libraries and systemic biases.
• HTML Report Generation: Generates static HTML reports summarizing QC analyses and visualizations.

Scientific Applications:

• Quality Control in Large-Scale NGS Studies: Enables systematic QC assessment across large numbers of sequencing libraries and samples.
• Identification of Systemic Biases and Outliers: Uses multi-sample visualizations and clustering to detect library-specific issues and study-wide biases.
• Interpretation of QC Metrics for Downstream Analysis: Supports evaluation of QC metrics to inform decisions for downstream genomic analyses.

Methodology:

ngsReports leverages R's statistical and graphical capabilities to import FastQC and other NGS log files, integrate FastQC and Picard outputs, generate customizable QC visualizations, perform hierarchical clustering on QC metrics, and produce HTML reports.