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Bio workflows tcr pipeline

Skill FridrichMethod/awesome-skills/skills/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.From its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill bio-workflows-tcr-pipeline

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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SKILL.md

2.0 KB, 480 tokens by cl100k_base, as published. Nobody here has run it

<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

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
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it: 2 files

3.7 KB alongside SKILL.md, 1 of them executable

examples/

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