LymAnalyzer

LymAnalyzer analyzes next-generation sequencing (NGS) and deep sequencing data to profile immunoglobulins (IGs) and T cell receptors (TCRs) and to identify novel gene-segment alleles for characterization of adaptive immune diversity.

Key Features:

• IG and TCR repertoire profiling: Profiles immunoglobulin (IG) and T cell receptor (TCR) repertoires from NGS and deep sequencing data to improve completeness and accuracy of repertoire characterization.
• Novel allele identification: Implements procedures for identifying novel alleles of gene segments.
• Validation on datasets: Has been tested on both real and simulated datasets to evaluate performance.
• Cross-species applicability: Applicable to human and mouse data and to other species given an appropriate reference gene database.
• Implementation: Implemented in Java.

Scientific Applications:

• Adaptive immune repertoire analysis: Quantitative and qualitative analysis of IG and TCR diversity from deep sequencing datasets.
• Reference database refinement: Discovery of novel gene-segment alleles to enhance and expand reference gene databases.
• Comparative immunology: Comparative repertoire studies across human, mouse, and other species with available reference gene databases.
• Method validation and benchmarking: Use of real and simulated datasets for tool validation and benchmarking of repertoire analyses.

Methodology:

Profiles repertoires from NGS/deep sequencing data and applies procedures to identify novel gene-segment alleles, with validation performed on real and simulated datasets.