IMSEQ

IMSEQ assigns clonotypes from next-generation sequencing (NGS) data of recombined T-cell receptor (TCR) and immunoglobulin (IG) genes to characterize T- and B-cell receptor repertoires.

Key Features:

• Error Awareness: Incorporates routines to handle errors arising from PCR amplification and sequencing artifacts to improve clonotype-calling accuracy.
• Clonotype Assignment: Assigns clonotypes by identifying V (variable) and J (joining) gene segments and the complementarity-determining region 3 (CDR3) sequence.
• Versatile Input Handling: Processes both single-end and paired-end sequencing data.
• Species and Gene Flexibility: Is generic with respect to species and gene of interest, allowing application across diverse organisms and receptor genes.
• Performance and Accuracy: Demonstrates high clonotyping accuracy, error correction, and runtime efficiency on simulated and real-world datasets.

Scientific Applications:

• T- and B-cell repertoire analysis: Characterizes repertoire composition and clonotype distributions from NGS data to study repertoire dynamics.
• Immune response and disease monitoring: Enables investigation of changes in receptor clone distributions to study immune responses, disease progression, and potential therapeutic interventions.

Methodology:

Implemented in C++ using the SeqAn library; incorporates error-aware routines for PCR amplification and sequencing artifacts; assigns clonotypes by V/J gene segment and CDR3 sequence identification; supports single-end and paired-end input.