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bio-tcr-bcr-analysis-mixcr-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-tcr-bcr-analysis-mixcr-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: mixcr analyze for end-to-end TCR/BCR extraction and clonotype assembly.
- Extract TCR/BCR clonotypes from my sequencing data" → Assemble immune receptor sequences from raw reads, identify V(D)J gene segments, and generate clonotype tables for repertoire analysis. CLI: mixcr analyze for end-to-end TCR/BCR extraction and clonotype assembly.
- Goal: Run end-to-end V(D)J alignment and clonotype assembly from raw FASTQ files in a single command.
- Approach: Use MiXCR's preset-based analyze command which chains alignment, assembly, and export steps automatically.
Source Doc
Excerpt From SKILL.md
Step-by-Step Workflow
Goal: Process immune repertoire data through individual alignment, refinement, assembly, and export stages for fine-grained control.
Approach: Chain MiXCR CLI steps sequentially: align reads to V(D)J references, refine UMIs and sort, assemble clonotypes, then export results.
Preset Protocols
| Protocol | Use Case |
|---|---|
generic-tcr-amplicon | TCR amplicon sequencing |
generic-bcr-amplicon | BCR amplicon sequencing |
generic-tcr-amplicon-umi | TCR amplicon with UMIs |
rnaseq-tcr | TCR extraction from bulk RNA-seq |
rnaseq-bcr | BCR extraction from bulk RNA-seq |
10x-vdj-tcr | 10x Genomics TCR enrichment |
10x-vdj-bcr | 10x Genomics BCR enrichment |
takara-human-tcr-v2 | Takara SMARTer kit |
Species Support
mixcr align --species human ...
mixcr align --species mmu ...
Use cases
- Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- vdjtools-analysis - Downstream diversity analysis
- scirpy-analysis - Single-cell VDJ integration
- repertoire-visualization - Visualize MiXCR output
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