IGLoo

IGLoo analyzes sequence data and assemblies derived from lymphoblastoid cell lines, characterizing somatic V(D)J recombination events and improving germline assembly quality of immunoglobulin heavy-chain loci.

Key Features:

• Somatic V(D)J recombination characterization: IGLoo identifies breakpoints and missing immunoglobulin genes in assemblies.
• Reassembly framework: IGLoo improves germline assembly quality by integrating information on somatic events and population structural variations in immunoglobulin loci.
• PacBio high-fidelity read support: IGLoo processes high-fidelity reads for analysis of immunoglobulin heavy-chain loci.

Scientific Applications:

• Lymphoblastoid cell line immunoglobulin profiling: IGLoo addresses technical challenges where immunoglobulin loci contain mixtures of germline and somatically recombined haplotypes.
• Human pangenome reference improvement: IGLoo improves representation of immunoglobulin heavy-chain assemblies in pangenome resources such as those from the Human Pangenome Reference Consortium.
• V(D)J recombination mechanism study: IGLoo provides insights into mechanisms, gene usage, and patterns of V(D)J recombination and causes of assembly artifacts.

Methodology:

IGLoo analyzes sequence data and assemblies derived from lymphoblastoid cell lines, characterizes somatic V(D)J recombination events, and implements a reassembly framework that integrates information on somatic events and population structural variations in immunoglobulin loci.