MiTCR statistics

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chevron_left V(D)J assignment CDR3 sequence identification Quality control chevron_right
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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


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  • person_outline Dmitriy Chudakov <>

Publication for MiTCR

MiTCR in publications

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

[…] miseq analysis as described in tcrβ library preparation., 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 […]

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

[…] 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 […]

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

[…] 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 […]

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

[…] systempiper package (additional file )., 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, […]

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

[…] have been summarized in previous reviews [, , –]. other methods, such as imseq [], tcrklass, imonitor [], lymanalyzer [] and rtrc [], have however emerged since. a popular tool is mixcr (previously mitcr), developed by bolotin et al. [], which allows for a highly customizable analysis of both tcr and immunoglobulin sequences. this is the tool we chose for our analysis, as its parameters may […]

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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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