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MiXCR specifications

Information


Unique identifier OMICS_08732
Name MiXCR
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Raw FASTQ
Output data VDJ alignments file, assembled clonotypes
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Commercial
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Bolotin Dmitry

Publication for MiXCR

MiXCR citations

 (33)
library_books

The human Vδ2+ T cell compartment comprises distinct innate like Vγ9+ and adaptive Vγ9 subsets

2018
Nat Commun
PMCID: 5932074
PMID: 29720665
DOI: 10.1038/s41467-018-04076-0

[…] te a hierarchy of 10 common sequences) and uncommon highly amplified sequences were included in the final analysis. For more detailed analysis of the TCR repertoire, datasets were processed using the MiXCR software package to further correct for PCR and sequencing errors. Diversity metrics, clonotype overlap and gene usage were plotted in R, by VDJTools. […]

library_books

Simple paired heavy and light chain antibody repertoire sequencing using endoplasmic reticulum microsomes

2018
Genome Med
PMCID: 5921987
PMID: 29703216
DOI: 10.1186/s13073-018-0542-5

[…] quality filtered and annotated to define the individual HC (IgM or IgG) and LC (IgK) isotypes. The annotated reads were aligned to the human Ig germline genes (IMGT annotation []) and clustered using MiXCR [] to determine the number of unique paired CDR3 clones (requiring ≥ 2 reads per pair) including correction of PCR errors. From the pre-immunization sample, we identified a total of 2200 and 484 […]

library_books

Peptide–MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen Reactive T Cell Populations

2018
PMCID: 5857646
PMID: 29483360
DOI: 10.4049/jimmunol.1700242

[…] CR gene usage was determined using reference sequences from the ImMunoGeneTics database (http://www.imgt.org), and all TCR gene segments were designated according to ImMunoGeneTics nomenclature using MiXCR software (v1.8.1) (). When cells were sorted from PBMCs for TCR sequencing, only sequences that were present in at least five reads were included in the analyses. Unless otherwise stated, we onl […]

library_books

Switching and loss of cellular cytokine producing capacity characterize in vivo viral infection and malignant transformation in human T lymphotropic virus type 1 infection

2018
PLoS Pathog
PMCID: 5828519
PMID: 29444188
DOI: 10.1371/journal.ppat.1006861

[…] MiXCR software [] with standard settings was used to identify TCR alpha and beta CDR3-containing reads present in the RNA sequencing data, generating a list of CDR3s (individual clones) and their rela […]

library_books

CCR8 Expression Defines Tissue Resident Memory T Cells in Human Skin

2018
PMCID: 5818732
PMID: 29427415
DOI: 10.4049/jimmunol.1701377

[…] ested, only one TCRβ amino acid sequence was shared between the CCR8+ and CCR8− fractions within the CD4+ and CD8+ T cell subsets (donor 26; ). To extend these findings with greater coverage, we used MiXCR software to assemble CDR3β sequences from the RNA-Seq data (). In line with our initial analysis, we found that the CCR8+ and CCR8− fractions were polyclonal and displayed similar levels of dive […]

library_books

Method for identification of condition associated public antigen receptor sequences

2018
eLife
PMCID: 5873893
PMID: 29533178
DOI: 10.7554/eLife.33050.015

[…] archived at https://github.com/elifesciences-publications/vdjRec/).We start with annotated TCR datasets (CDR3 amino acid sequence, V-segment, J-segment), one per donor. Such datasets are produced by MiXCR (), immunoseq (http://www.adaptivebiotech.com/immunoseq) and most other software for NGS repertoire data preprocessing. Data we used was in immunoseq format, publicly available from https://clie […]

Citations

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MiXCR institution(s)
Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic

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