mixcr

simplified cellranger for long-read data

In silico data and tests

MiXCR Clonotyping Block

Extract TCR and BCR clonotypes from raw sequencing data. Alignment against germline gene databases, error correction, receptor assembly, and clonotype grouping — turning FASTQ into a quantified repertoire with full QC.

Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation

A nextflow pipeline for TCR repertoire building with MiXCR

Imports V(D)J data from various formats, including MiXCR, immunoSeq, AiRR and more (bulk or single-cell) and normalizes them into one standard clonotype dataset that every downstream

Process scFv sequencing data, separating each construct into its VH chain, VL chain, and synthetic linker, then assembling and quantifying unique scFv clonotypes

TCR clonotype analysis using mixcr and immunarch.

Align amplicon sequencing reads against your own reference construct instead of a germline database. Used for synthetic antibody and TCR libraries where diversity is engineered into defined regions of a known scaffold, and reports per-sample clonotypes with full alignment QC.