ImmunoDataAnalyzer

ImmunoDataAnalyzer analyzes immunological next-generation sequencing (NGS) data to process and characterize T cell receptor (TCR) and immunoglobulin (IG) repertoires.

Key Features:

• Quality control: Performs quality control on NGS reads to support reliable downstream repertoire analysis.
• Automated pre-processing of barcoded and UMI-tagged data: Performs automated pre-processing of barcoded and unique molecular identifier (UMI) tagged NGS data.
• Integration of curated repertoire tools: Integrates functionalities from a curated selection of immune repertoire analysis software into a unified workflow.
• Clonotype assembly and metrics: Assembles clonotypes from raw NGS reads and computes clonality, diversity measures, V(D)J gene segment usage, clonotype overlap, and between-sample similarity.
• Visualization and reporting: Produces compact summary reports that include visualizations, calculations, and sample-level results.
• Machine learning output generation: Generates output files and key figures suitable for input to machine learning frameworks to model traits across samples.
• Comparative repertoire analysis: Facilitates descriptive data analysis and comparison of multiple immune repertoires.
• Contamination and sample-swap detection: Detects sample swaps and cross-sample contamination arising during sample preparation.

Scientific Applications:

• Repertoire characterization: Characterizes TCR and IG repertoires by quantifying clonality, diversity, and V(D)J gene segment usage.
• Comparative immunology: Compares immune repertoires across samples or cohorts to assess similarity and clonotype overlap.
• Immune response analysis: Supports analysis of immune responses and immunological behavior using high-throughput NGS data.
• Machine learning-driven trait modeling: Provides feature sets and figures for machine learning frameworks to model traits across samples.
• Data integrity monitoring: Detects and flags sample swaps and cross-sample contamination to preserve dataset integrity.

Methodology:

Performs automated quality control and pre-processing of barcoded and UMI-tagged NGS data, assembles clonotypes from raw reads, computes clonality, diversity measures, V(D)J gene segment usage and between-sample similarity, generates output files with key figures, and detects sample swaps and cross-sample contamination.