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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>`).

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

Table of contents:

.. toctree::
   :hidden:
   :maxdepth: 1

   install
   quickstart
   align
   assemble
   export
   newAligner
   importSegments
   geneFeatures
   appendix
   license