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bio-tcr-bcr-analysis-mixcr-analysis

Align TCR/BCR sequencing reads and assemble clonotypes with MiXCR.

Updated Mar 30, 2026
Search Tags:#tcr#data-analysis#clonotype#bcr#vdj#mixcr#immune-repertoire
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-tcr-bcr-analysis-mixcr-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-tcr-bcr-analysis-mixcr-analysis
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-tcr-bcr-analysis-mixcr-analysis
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-tcr-bcr-analysis-mixcr-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR to identify clonotypes and their frequencies.

Core Features & Use Cases

  • End-to-end V(D)J analysis: align reads to reference, refine/assemble clonotypes, and export clonotype tables with V/D/J usage and CDR3 sequences.
  • Supports multiple data types and presets (amplicon, 10x VDJ) for bulk and single-cell repertoires, with Python-ready outputs.
  • Python integration: parse MiXCR outputs into pandas-friendly data frames for downstream analyses.

Quick Start

Run MiXCR analysis on your TCR/BCR sequencing data to align reads, assemble clonotypes, and export results.

Frequently Asked Questions about bio-tcr-bcr-analysis-mixcr-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I analyze TCR and BCR sequencing data to identify clonotypes?▼

MiXCR supports single-cell immune repertoire analysis through its 10x VDJ presets. It aligns reads, refines clonotypes, and exports CDR3 sequences specifically for single-cell repertoires.

Can I use MiXCR presets for 10x VDJ single-cell data?▼

MiXCR supports single-cell immune repertoire analysis through its 10x VDJ presets. It aligns reads, refines clonotypes, and exports CDR3 sequences specifically for single-cell repertoires.

What do I need to perform V(D)J alignment and clonotype assembly?▼

MiXCR exports clonotype tables that can be parsed into pandas-friendly data frames for Python integration. This allows you to directly use the clonotype data, including CDR3 sequences, in downstream Python analyses.

How do I export MiXCR clonotype tables for Python downstream analysis?▼

MiXCR exports clonotype tables that can be parsed into pandas-friendly data frames for Python integration. This allows you to directly use the clonotype data, including CDR3 sequences, in downstream Python analyses.

Does MiXCR support both bulk and single-cell immune repertoire pipelines?▼

MiXCR requires appropriate species references to accurately align reads and assemble clonotypes. Without the correct species references, the V(D)J alignment and clonotype assembly process will not function properly.

Do I need specific species references for V(D)J alignment?▼

MiXCR requires appropriate species references to accurately align reads and assemble clonotypes. Without the correct species references, the V(D)J alignment and clonotype assembly process will not function properly.

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