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BioSkills bio-workflows-tcr-pipeline

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.

install
source · Clone the upstream repo
git clone https://github.com/GPTomics/bioSkills
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/GPTomics/bioSkills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/workflows/tcr-pipeline" ~/.claude/skills/gptomics-bioskills-bio-workflows-tcr-pipeline && rm -rf "$T"
manifest: workflows/tcr-pipeline/SKILL.md
source content

Version Compatibility

Reference examples tested with: MiXCR 4.6+, VDJtools 1.2.1+

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

  • 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.

TCR/BCR Analysis Pipeline

"Analyze my TCR/BCR repertoire sequencing data end-to-end" → Orchestrate MiXCR clonotype extraction, VDJtools diversity/repertoire analysis, Immcantation SHM and lineage analysis, and visualization of V/J gene usage and clonal dynamics.

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