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importSegments.rst

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Using external libraries for alignment

Tip

MiXCR utilases libraries in .json format (see https://github.com/repseqio for details).

Note

In some cases when using an external library mixcr will try to establish connection with NCBI over the internet.

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 ~/.mixcr/libraries folder, to the directory from where mixcr is started or to libraries/ subfolder of mixcr installation folder.

Tip

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

... Building alignments

--library option specifies the library to use for alignment. 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 assemble alignments.vdjca clones.clns

... Assembling clones

> mixcr exportClones --chains IGH clones.clns clones.txt

... Exporting clones to tab-delimited file