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Using external library

MiXCR has a built-in set of reference libraries that were carefully created by our team. However, one can use other external libraries, such as IMGT or any other. These libraries have to be property compiled to use with MiXCR.

Using IMGT library

Compiled IMGT library file for MiXCR can be downloaded at In order to use the library put the .json library file to one of the following locations:

  • ~/.mixcr/libraries folder
  • the directory from where mixcr is started
  • libraries/ subfolder of mixcr installation folder

Use mixcr -v to see what folders mixcr uses to look for library .json file.

> mixcr -v
Library search path:
- built-in libraries
- /home/username/.
- /home/username/.mixcr/libraries
- /software/mixcr/libraries

Option --library specifies the library to use for mixcr align. If the short name is given (ex.–library imgt) mixcr will look for the latest version in the folder. Otherwise, to use one of the old versions give the full name including the version number (ex. -library imgt.201631-4)


> mixcr align --library imgt input_R1.fastq input_R2.fastq alignments.vdjca