generated: '2026-07-20'
method: searched
source: https://mixcr.com/mixcr/reference/
name: MiXCR
description: >-
  MiXCR is MiLaboratories' command-line software platform for analysis of
  Next-Generation Sequencing (NGS) data for immune profiling — T-cell receptor
  (TCR) and immunoglobulin (IG / antibody) repertoire sequencing. It runs as a
  JVM command-line tool that takes raw FASTQ through alignment, clonotype
  assembly, and export.
docs: https://mixcr.com/mixcr/reference/
install:
  - method: binary
    detail: Binary distributions (zip) from GitHub releases.
    url: https://github.com/milaboratory/mixcr/releases
  - method: docker
    detail: Official Docker image.
    url: https://mixcr.com/
license_note: >-
  Free for academic / non-commercial use; a commercial license is required for
  industry use (https://licensing.milaboratories.com).
commands:
  - name: analyze
    group: pipeline
    description: Run a complete upstream analysis pipeline (align + assemble + export) from a preset.
    docs: https://mixcr.com/mixcr/reference/mixcr-analyze/
  - name: align
    group: pipeline
    description: Align raw sequencing reads (FASTQ/FASTA/BAM/SAM) to reference V/D/J/C libraries.
    docs: https://mixcr.com/mixcr/reference/mixcr-align/
  - name: assemble
    group: pipeline
    description: Assemble clonotypes from alignments into a compressed .clns / .clna file.
    docs: https://mixcr.com/mixcr/reference/mixcr-assemble/
  - name: assemblePartial
    group: pipeline
    description: Assemble partially-overlapping alignments.
  - name: assembleContigs
    group: pipeline
    description: Assemble full receptor contigs from clonotype alignments.
  - name: extend
    group: pipeline
    description: Impute germline sequences to extend incomplete alignments.
  - name: exportClones
    group: export
    description: Export clonotype tables to tab-delimited files.
    docs: https://mixcr.com/mixcr/reference/mixcr-export/
  - name: exportClonesPretty
    group: export
    description: Export clonotypes in human-readable form.
  - name: exportAlignments
    group: export
    description: Export alignment tables.
  - name: exportAirr
    group: export
    description: Export results in AIRR-community (rearrangement) TSV format.
  - name: exportQc
    group: export
    description: Export quality-control reports.
  - name: exportPlots
    group: export
    description: Export publication-ready plots.
  - name: findAlleles
    group: analysis
    description: Infer individual germline alleles across a dataset.
  - name: findShmTrees
    group: analysis
    description: Reconstruct somatic hypermutation (SHM) lineage trees.
  - name: downsample
    group: analysis
    description: Downsample datasets for normalized comparison.
  - name: qc
    group: analysis
    description: Run quality-control checks on results.
key_flows:
  - name: FASTQ to clonotype table
    steps: [align, assemble, exportClones]
  - name: One-shot preset analysis
    steps: [analyze]