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MiXCR: a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.

MiXCR is free for academic and non-profit use (see :ref:`License <license>`).

_static/mixcr.png

MiXCR pipeline. The workflow from IG or T-cell receptor data sets to final clonotypes is shown

.. toctree::
   :hidden:
   :caption: Getting started
   :maxdepth: 3

   install
   quickstart

.. toctree::
   :hidden:
   :caption: Main actions
   :maxdepth: 1

   align
   assemble
   export

.. toctree::
   :hidden:
   :caption: Special cases
   :maxdepth: 1

   rnaseq
   importSegments
   newAligner

.. toctree::
   :hidden:
   :caption: In-depth topics
   :maxdepth: 1

   geneFeatures
   appendix
   utils
   license