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 toi be property compiled to use with MiXCR.
Using IMGT library
Compiled IMGT library file for MiXCR can be downloaded at https://github.com/repseqio/library-imgt/releases. In order to use the library put the
.json library file to one of the following locations:
- the directory from where mixcr is started
- libraries/ subfolder of mixcr installation folder
mixcr -v to see what folders mixcr uses to look for library
> mixcr -v ... Library search path: - built-in libraries - /home/username/. - /home/username/.mixcr/libraries - /software/mixcr/libraries
--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.
> mixcr align --library imgt input_R1.fastq input_R2.fastq alignments.vdjca