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Bio Tcr Bcr Analysis Mixcr Analysis by tools-only

Name: Bio Tcr Bcr Analysis Mixcr Analysis
Rating: 4.2 (5 reviews)
Author: tools-only

Bio Tcr Bcr Analysis Mixcr Analysis

Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.

tools-only Updated Sep 22, 2026 7 repo stars

File contents

MiXCR Analysis

Complete Workflow (Recommended)

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

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

Step 2: Refine and Assemble

mixcr refineTagsAndSort alignments.vdjca alignments_refined.vdjca

mixcr assemble alignments_refined.vdjca clones.clns

Step 3: Export Results

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

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

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

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

---name: bio-tcr-bcr-analysis-mixcr-analysis-2description: Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.---# MiXCR Analysis## Complete Workflow (Recommended)```bashmixcr 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_prefixmixcr analyze 10x-vdj-tcr \ input_R1.fastq.gz input_R2.fastq.gz \ output_prefix```## Step-by-Step Workflow### Step 1: Align Reads```bashmixcr align \ --species human \ --preset generic-tcr-amplicon-umi \ input_R1.fastq.gz input_R2.fastq.gz \ alignments.vdjcamixcr align \ --species human \ --rna \ -OallowPartialAlignments=true \ input_R1.fastq.gz input_R2.fastq.gz \ alignments.vdjca```### Step 2: Refine and Assemble```bashmixcr refineTagsAndSort alignments.vdjca alignments_refined.vdjcamixcr assemble alignments_refined.vdjca clones.clns```### Step 3: Export Results```bashmixcr exportClones \ --chains TRB \ --preset full \ clones.clns \ clones.tsvmixcr 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```bashmixcr 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```bashmixcr 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```pythonimport pandas as pddef 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

Frequently asked questions