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MiTCR specifications


Unique identifier OMICS_00003
Name MiTCR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Dmitriy Chudakov

Publication for MiTCR

MiTCR citations


MAIT cell clonal expansion and TCR repertoire shaping in human volunteers challenged with Salmonella Paratyphi A

Nat Commun
PMCID: 5772558
PMID: 29343684
DOI: 10.1038/s41467-017-02540-x

[…] The sequencing files generated by the MiSeq were split based on their barcoded sequence using Jemultiplexer (GBCS) and then run through the MiTCR software, aligning TCRα/β sequences using default parameters. VDJ Tools was then used to filter out the non-functional sequences prior to post-analysis visualization. Clonotypes were defined bas […]


iRAGu: A Novel Inducible and Reversible Mouse Model for Ubiquitous Recombinase Activity

Front Immunol
PMCID: 5686385
PMID: 29176980
DOI: 10.3389/fimmu.2017.01525

[…] Original raw paired reads were quality filtered with seqtk (trimfq-q 0.01) and merged with flash. Both merged and unmerged reads were pooled together to pass to the MiTCR software version 1.0.3 (), using the following command: java-jar-Xmx2G-jar mitcr.jar-pset flex-species mm-gene TCRab_S1S5_filtered_001.all.fastq TCRab_S1S5_filtered_001.all.mitcr.cls, where TCRa […]


A novel signature for stratifying the molecular heterogeneity of the tissue infiltrating T cell receptor repertoire reflects gastric cancer prognosis

Sci Rep
PMCID: 5552765
PMID: 28798410
DOI: 10.1038/s41598-017-08289-z

[…] ified product was then sequenced.The raw data were cleaned using Trimmomatic v0.33. We then used FLASH v1.2.11 to merge the paired reads and to obtain the complete sequences of the TCRβ CDR3 regions. MiTCR was used to assign the rearranged mRNA sequences to their germline V, D, and J counterparts. The basic statistical and diversity analyses (calculation of ShannonDI) of the T-cell clones were acc […]


Immunology repertoire study of pulmonary sarcoidosis T cells in CD4+, CD8+ PBMC and tissue

PMCID: 5685688
PMID: 29163767
DOI: 10.18632/oncotarget.20085

[…] s were merged by aligning the head part of the sequence (BGI developed software FqMerger). In this way, we obtained the merged contig sequences and the length distribution plot. Subsequently, we used miTCR, developed by MiLaboratory ( for the alignment. This program has an automated adjustment mechanism for errors introduced by sequencing and PCR and will p […]


V J combinations of T cell receptor predict responses to erythropoietin in end stage renal disease patients

J Biomed Sci
PMCID: 5504791
PMID: 28697735
DOI: 10.1186/s12929-017-0349-5

[…] The resulting FASTA files were subjected to CDR3β extraction, V, D, and J regions mapping, clonotype identification of PCR, and sequencing errors with using MiTCR software [] with the following parameters: ‘species = hs’ and ‘gene = TRB’. A phred quality score of >25 was set as the threshold value for each base within the CDR3 region. In addition, we used […]


Overview of methodologies for T cell receptor repertoire analysis

BMC Biotechnol
PMCID: 5504616
PMID: 28693542
DOI: 10.1186/s12896-017-0379-9

[…] her tool that provides TCR diversity measures and gene usage statistics computations is the R package “tcR”, which can be used to process the output files format of software as ImmunoSEQ [, ], IMSEQ, MiTCR, MiXCR, MIGEC and VDJtools []. Other approaches recently developed for estimation of TCR diversity are from Greiff et al., which creates a diversity profile using many diversity coefficients sim […]


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MiTCR institution(s)
Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
MiTCR funding source(s)
Supported by the Molecular and Cell Biology program of the Russian Academy of Sciences and Russian Foundation for Basic Research (12-04-33139-mol-a, 12-04-33065-mol-a, 12-04-00229-a, 13-04-00998-a and 13-04-40251).

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