The protocols in this section describe how to extract T- and B- Cell receptor repertoire from NGS data generated from Cellecta DriverMap AIR DNA kit. MiXCR is used to analyze NGS data, extract clonotype and obtain vector plots and tabular results.
Even though MiXCR is widely used for immune repertoires data analysis. Other bioinformatics tools/frameworks are also developed to analyze immune repertoires.
| Tools | Published year | Aligner | Website |
|---|---|---|---|
| IMGT/HighV-QUEST | 2012 | GPA (NW) | https://www.imgt.org/IMGTindex/IMGTHighV-QUEST.php |
| IgBLAST | 2013 | BLAST | https://www.ncbi.nlm.nih.gov/igblast/ |
| IMSEQ | 2015 | SCF matching | http://www.imtools.org/ |
| LymAnalyzer | 2015 | Fast-tag | https://sourceforge.net/projects/lymanalyzer/ |
The procedures for data processing and analysis assume you already have the necessary software installed. Appendix C provides links and guidance to help you set up the necessary software on your system if they are not installed. Cellecta does not own any of these software packages and is not responsible for maintaining them, and the installation instructions we provide are for convenience only.
MiXCR is free for academic and non-profit use (see License). The commercial license can be requested at https://licensing.milaboratories.com or by email to licensing@milaboratories.com or https://milaboratories.com/contacts. Before downloading or accessing the software, please read the License Agreement available at: https://github.com/milaboratory/mixcr/blob/develop/LICENSE.
Mac OS and Linux OS are recommended for data processing and analysis.
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