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TCRklass

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Identifies variable (V) and joining (J) segments, as well as CDR3 region sequences using K-string-based algorithm for translated nucleotide queries. Specifically designed to handle short reads, the tool correctly accounts for sequencing reads with missing CDR3 region in order to provide an unbiased V/J segment usage data.

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TCRklass classification

TCRklass specifications

Software type:: Package/Module
Restrictions to use:: None
Operating system:: Unix/Linux, Mac OS, Windows
License:: GNU General Public License version 2.0
Stability:: Stable

Interface:: Command line interface
Biological technology:: Illumina
Programming languages:: C++, Perl
Computer skills:: Advanced
Maintained:: Yes
Issue URL:: https://sourceforge.net/p/tcrklass/tickets/

Credits

Publications

Publications contributions

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(Yang et al., 2015) TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization. J Immunol.
PMID: 25404364

Institution(s)

Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

Link to literature

Methodology

(Heather et al., 2017) High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform.
PMID: 28077404

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