AgentSkillsCN

bio-workflows-tcr-pipeline

从 FASTQ 到克隆型多样性指标的全流程 TCR/BCR 克隆谱分析工作流。适用于分析来自批量实验或单细胞实验的免疫克隆谱测序数据时使用。

SKILL.md
--- frontmatter
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

TCR/BCR Analysis Pipeline

Pipeline Overview

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

Step 1: MiXCR Processing

bash
# 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

bash
# 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

bash
# 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