Bio Workflows Tcr Pipeline
- 3 installs
- 1.1k repo stars
- Updated July 25, 2026
- gptomics/bioskills
Run an end-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics using MiXCR and VDJtools.
About
Orchestrates MiXCR V(D)J alignment, clonotype assembly, and VDJtools diversity metrics for immune repertoire sequencing. A developer uses it to analyze bulk or single-cell TCR/BCR data into clonotype and diversity output.
- MiXCR align, assemble, and export of V(D)J clonotypes
- VDJtools diversity metrics and repertoire visualization
Bio Workflows Tcr Pipeline by the numbers
- 3 all-time installs (skills.sh)
- Ranked #1,661 of 2,064 Data Science & ML skills by installs in the Skillselion catalog
- Data as of Aug 5, 2026 (Skillselion catalog sync)
npx skills add https://github.com/gptomics/bioskills --skill bio-workflows-tcr-pipelineAdd your badge
Show developers this skill is listed on Skillselion. Paste this into your README.
| Installs | 3 |
|---|---|
| repo stars | ★ 1.1k |
| Last updated | July 25, 2026 |
| Repository | gptomics/bioskills ↗ |
What it does
Run an end-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics using MiXCR and VDJtools.
Files
TCR/BCR Analysis Pipeline
Pipeline Overview
FASTQ → MiXCR align → Assemble → Export → VDJtools diversity → VisualizationStep 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.txtStep 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
Related skills
Microsoft FoundryDeploy, evaluate, and continuously improve Microsoft Foundry agents from a single agent interface.490k1.3k
Ai Research ReproductionOrchestrate trustworthy, auditable reproduction of deep learning repositories directly from their READMEs.176k511Run TrainSafely execute selected deep learning training commands with standardized evidence capture.176k511Explore RunSafely run isolated exploratory experiments with clear recording and conservative selection before committing changes.176k511Paper Context ResolverFetch precise reproduction-critical details like dataset splits, preprocessing steps, or evaluation protocols from the original academic paper when the repo README leav141k511Repo Intake And PlanScan unfamiliar AI research repositories and receive a minimal, trustworthy reproduction target before investing significant time.140k511