MiXCR

MiXCR is a software package used for the analysis of immune repertoire sequencing data. It is designed to process raw sequencing reads from various high-throughput platforms and reconstruct the sequences of T-cell receptors (TCRs) and B-cell receptors (BCRs), also known as immunoglobulins. The primary goal of MiXCR is to identify and quantify the different receptor clonotypes present in a biological sample.

The workflow of MiXCR typically involves several steps. First, it performs read assembly to reconstruct the full V(D)J gene sequences from fragmented reads. It then identifies the V, D, and J gene segments that rearranged to form the receptor. Following gene identification, MiXCR determines the complementary determining region 3 (CDR3), which is a critical determinant of antigen specificity. Finally, it quantifies the abundance of each unique clonotype.

MiXCR supports various sequencing protocols, including those targeting TCR alpha, beta, gamma, and delta chains, as well as BCR heavy and light chains. The software is known for its accuracy, speed, and flexibility, allowing researchers to analyze large datasets and perform downstream analyses such as assessing repertoire diversity, identifying public and private clonotypes, and comparing repertoires across different samples or conditions. It is widely used in immunology research, cancer immunotherapy, and infectious disease studies. MiXCR is available as a command-line tool and can be integrated into larger bioinformatics pipelines.