MiXCR Analysis (bioSkills)

A Claude Code skill that aligns raw immune-repertoire sequencing reads and assembles TCR/BCR clonotypes with MiXCR, choosing and auditing the correct chemistry-matched preset.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — MiXCR itself requires a separate license (free for academic/non-commercial use)
Capabilities Read/Write — Claude runs the skill’s workflow locally (Bash/Python), not as an MCP tool
Verified works · 2026-07-20
Security caution · 2026-07-20 — skill provenance matches GPTomics/bioSkills, MIT, directory confirmed this run, but the required MiXCR binary is separately licensed (free academic/non-commercial only)

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

  • Claude Code — clone and install via the bundled script: 
    git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "tcr-bcr-analysis"

    The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/tcr-bcr-analysis/mixcr-analysis ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). The skill declares MiXCR (v4.7+) as its external dependency in SKILL.md; install and license it when prompted on first use.

What it does

Runs the MiXCR 4.7+ analysis pipeline for TCR/BCR repertoire profiling, aligning reads to V(D)J germline segments, collapsing molecules/cells by barcode, and assembling clonotypes keyed on CDR3 plus V and J genes:

  • Preset selection matched to wet-lab chemistry — 5’RACE/template-switch vs multiplex-primer amplicon (rigid vs floating boundaries), RNA vs gDNA (--rna/--dna), bulk vs 10x single-cell, UMI vs no-UMI, and kit presets (Takara, NEBNext, QIAseq, BD, MiLaboratory).
  • Pipeline stages — align → refineTagsAndSort → assemblePartial → extend → assemble → assembleCells → export.
  • Quantitation choices — reads vs UMI vs cell denominator.
  • Export — native MiXCR fields or AIRR rearrangement TSV (exportAirr) for downstream Immcantation/scirpy/VDJtools, plus alignment/chain-usage QC (exportQc).

Primary use cases: bulk and single-cell TCR/BCR clonotype assembly, preset auditing for a library chemistry, AIRR export for downstream repertoire analysis.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally via Bash/Python rather than as an MCP server. The upstream skill front-matter name is bio-tcr-bcr-analysis-mixcr-analysis; if you invoke it as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /mixcr-analysis. MiXCR requires its own license — free for academic/non-commercial use, obtained from MiLaboratories; the skill’s MIT license covers only the workflow instructions, not MiXCR itself. Downstream analysis of the AIRR export is handled by immcantation-analysis (bulk) or scirpy-analysis (single-cell). Upstream directory: tcr-bcr-analysis/mixcr-analysis.

Sources

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.