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.

bash
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

bash
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

Step 2: Refine and Assemble

bash
mixcr refineTagsAndSort alignments.vdjca alignments_refined.vdjca

mixcr assemble alignments_refined.vdjca clones.clns

Step 3: Export Results

bash
mixcr exportClones \
    --chains TRB \
    --preset full \
    clones.clns \
    clones.tsv

mixcr exportClones \
    --chains TRB \
    -cloneId -readCount -readFraction \
    -nFeature CDR3 -aaFeature CDR3 \
    -vGene -dGene -jGene \
    clones.clns \
    clones_custom.tsv

Preset Protocols

| Protocol | Use Case | |----------|----------| | generic-tcr-amplicon | TCR amplicon sequencing | | generic-bcr-amplicon | BCR amplicon sequencing | | generic-tcr-amplicon-umi | TCR amplicon with UMIs | | rnaseq-tcr | TCR extraction from bulk RNA-seq | | rnaseq-bcr | BCR extraction from bulk RNA-seq | | 10x-vdj-tcr | 10x Genomics TCR enrichment | | 10x-vdj-bcr | 10x Genomics BCR enrichment | | takara-human-tcr-v2 | Takara SMARTer kit |

Species Support

bash
mixcr align --species human ...
mixcr align --species mmu ...

# Available: human, mmu, rat, rhesus, dog, pig, rabbit, chicken

Output Format

| Column | Description | |--------|-------------| | cloneId | Unique clone identifier | | readCount | Number of reads | | cloneFraction | Proportion of repertoire | | nSeqCDR3 | Nucleotide CDR3 sequence | | aaSeqCDR3 | Amino acid CDR3 sequence | | allVHitsWithScore | V gene assignments | | allDHitsWithScore | D gene assignments | | allJHitsWithScore | J gene assignments |

Quality Metrics

Goal: Assess alignment and assembly quality to identify problematic samples.

Approach: Export MiXCR alignment reports and check key success rate metrics.

bash
mixcr exportReports alignments.vdjca

# Key metrics:
# - Successfully aligned reads (>80% is good)
# - CDR3 found (>70% of aligned)
# - Clonotype count (varies by sample type)

Parse MiXCR Output in Python

Goal: Load MiXCR clonotype tables into pandas for downstream analysis and integration.

Approach: Read tab-delimited export files and rename columns to standardized names.

python
import pandas as pd

def load_mixcr_clones(filepath):
    df = pd.read_csv(filepath, sep='\t')
    df = df.rename(columns={
        'readCount': 'count',
        'cloneFraction': 'frequency',
        'aaSeqCDR3': 'cdr3_aa',
        'nSeqCDR3': 'cdr3_nt'
    })
    return df

Related Skills

• vdjtools-analysis - Downstream diversity analysis
• scirpy-analysis - Single-cell VDJ integration
• repertoire-visualization - Visualize MiXCR output