name: bio-workflows-tcr-pipeline description: End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments. tool_type: cli primary_tool: MiXCR measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

TCR/BCR Analysis Pipeline

Pipeline Overview

FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → Visualization

Step 1: MiXCR Processing

# Align reads to V(D)J segments
mixcr align -s hsa -p rna-seq \
    R1.fastq.gz R2.fastq.gz \
    aligned.vdjca

# Assemble clonotypes
mixcr assemble aligned.vdjca clones.clns

# Export
mixcr exportClones clones.clns clones.txt

Step 2: VDJtools Analysis

# Convert to VDJtools format
vdjtools Convert -S mixcr clones.txt vdjtools/

# Diversity metrics
vdjtools CalcDiversityStats vdjtools/clones.txt diversity/

# Sample overlap
vdjtools CalcPairwiseDistances vdjtools/*.txt overlap/

Step 3: Visualization

# Spectratype plot
vdjtools PlotFancySpectratype vdjtools/clones.txt spectra/

# V usage
vdjtools PlotFancyVJUsage vdjtools/clones.txt usage/

QC Checkpoints

1. After alignment: Check V/J assignment rate (>70% typical)
2. After assembly: Verify clonotype count and coverage
3. After diversity: Compare metrics to expected range

Related Skills

• tcr-bcr-analysis/mixcr-analysis - Detailed MiXCR usage
• tcr-bcr-analysis/vdjtools-analysis - Diversity metrics
• tcr-bcr-analysis/repertoire-visualization - Plots