VDJviz

VDJviz analyzes T- and B-cell receptor sequencing (Rep-Seq) data to perform repertoire analysis and quality control for immunogenomic studies.

Key Features:

• Versatile Data Handling: Processes outputs from various Rep-Seq pre-processing software and datasets generated by high-throughput sequencing.
• Quality Control: Performs quality-control checks on Rep-Seq data to identify technical and analytical artifacts.
• Spectratype Exploration: Analyzes CDR3 length distributions and frequencies to characterize spectratypes.
• Clonality Assessment: Evaluates repertoire clonality to assess diversity and clonal expansion.
• V-(D)-J Recombination Patterns: Analyzes V-(D)-J recombination patterns to characterize antigen receptor formation.
• Shared Clonotype Identification: Identifies shared clonotypes across samples to support comparative analyses.
• Bias Detection: Detects biases including artificial inflation of repertoire diversity and potential cross-sample contamination.

Scientific Applications:

• Immunogenomics Research: Characterization of adaptive immune repertoires from T- and B-cell receptor sequencing for immunogenomic studies.
• Antigen Specificity and Immune Memory: Investigation of antigen specificity and immune memory through analysis of receptor sequences and clonotype distributions.
• Clinical and Comparative Studies: Supporting studies of immune responses in health and disease via quality control and comparative repertoire analysis.

Methodology:

Processes outputs of Rep-Seq pre-processing software and performs quality-control, spectratype (CDR3 length distribution), clonality evaluation, V-(D)-J recombination analysis, shared clonotype identification, and bias detection (artificial diversity, cross-sample contamination).