Version Compatibility

Reference examples tested with: MiXCR 4.6+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

MiXCR Analysis

"Extract TCR/BCR clonotypes from my sequencing data" → Assemble immune receptor sequences from raw reads, identify V(D)J gene segments, and generate clonotype tables for repertoire analysis.

• CLI: mixcr analyze for end-to-end TCR/BCR extraction and clonotype assembly

Complete Workflow (Recommended)

Goal: Run end-to-end V(D)J alignment and clonotype assembly from raw FASTQ files in a single command.

Approach: Use MiXCR's preset-based analyze command which chains alignment, assembly, and export steps automatically.

mixcr analyze generic-tcr-amplicon \
    --species human \
    --rna \
    --rigid-left-alignment-boundary \
    --floating-right-alignment-boundary C \
    input_R1.fastq.gz input_R2.fastq.gz \
    output_prefix

mixcr analyze 10x-vdj-tcr \
    input_R1.fastq.gz input_R2.fastq.gz \
    output_prefix

Step-by-Step Workflow

Goal: Process immune repertoire data through individual alignment, refinement, assembly, and export stages for fine-grained control.

Approach: Chain MiXCR CLI steps sequentially: align reads to V(D)J references, refine UMIs and sort, assemble clonotypes, then export results.

Step 1: Align Reads

mixcr align \
    --species human \
    --preset generic-tcr-amplicon-umi \
    input_R1.fastq.gz input_R2.fastq.gz \
    alignments.vdjca

mixcr align \
    --species human \
    --rna \
    -OallowPartialAlignments=true \
    input_R1.fastq.gz input_R2.fastq.gz \
    alignments.vdjca