The protocols in this section describe how to extract T- and B- Cell receptor repertoire from NGS data generated from the Cellecta DriverMap AIR 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 | https://www.imtools.org/ |
| LymAnalyzer | 2015 | Fast-tag | https://sourceforge.net/projects/lymanalyzer/ |
MiXCR is free for academic and non-profit use (see License). The commercial license could be requested at https://licensing.milaboratories.com or by email to licensing@milaboratories.com or https://milaboratories.com/contacts. Please refer to Appendix C for installing instructions. Before downloading or accessing the software, please carefully 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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