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MiTCR specifications

Information


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

Versioning


No version available

Documentation


Maintainer


  • person_outline Dmitriy Chudakov <>

Publication for MiTCR

MiTCR citations

 (20)
library_books

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

2018
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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 (http://mitcr.milaboratory.com/downloads/) for the alignment. this program has an automated adjustment mechanism for errors introduced by sequencing and pcr […]

library_books

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

2017
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, […]

library_books

Overview of methodologies for T cell receptor repertoire analysis

2017
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 […]

library_books

CD8+ T cells specific for the islet autoantigen IGRP are restricted in their T cell receptor chain usage

2017
PMCID: 5353542
PMID: 28300170
DOI: 10.1038/srep44661

[…] using next generation sequencing as previously described. libraries containing < 0.5 mio reads were excluded. tcr cdr3 region sequence extraction and pcr error correction was performed with mitcr. all additional sequence analysis was conducted in knime 2.11.2., flu mp58-66- and igrp265-273-specific cd8+ t cell clones were propagated from multimer positive single cells according […]


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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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