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Protocols

VDJtools specifications

Information


Unique identifier OMICS_08095
Name VDJtools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Pre-processed RepSeq data
Output data RepSeq analysis results
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
License Artistic License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Mikhail Shugay

Publication for VDJtools

VDJtools citations

 (17)
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

[…] he 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

Human γδ T Cell Receptor Repertoires in Peripheral Blood Remain Stable Despite Clearance of Persistent Hepatitis C Virus Infection by Direct Acting Antiviral Drug Therapy

2018
Front Immunol
PMCID: 5864898
PMID: 29616028
DOI: 10.3389/fimmu.2018.00510

[…] the given sample. All bioinformatics analysis was conducted using R (version 3.2.2) and bash shell commands. Shannon indices were calculated with the R library “vegan” and Morisita–Horn indices with VDJtools () and TcR (). Analysis scripts are available upon request. […]

call_split

T Cell Phenotype and T Cell Receptor Repertoire in Patients with Major Depressive Disorder

2018
Front Immunol
PMCID: 5826233
PMID: 29515587
DOI: 10.3389/fimmu.2018.00291
call_split See protocol

[…] T cell clones. Raw sequence data were pre-processed by Adaptive Biotechnologies for PCR and sequencing error correction () and uploaded into the immunoSEQ® Analyzer. Post-analysis was conducted using VDJtools v1.0.7 (). Sequencing data are available using the following URL: http://doi.org/10.21417/B7RG6H. […]

library_books

CCR8 Expression Defines Tissue Resident Memory T Cells in Human Skin

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

[…] uenced, and analyzed as described previously (). Assembly of TCR sequences from short-read RNA-Seq data was performed using MiXCR software (), and postassembly repertoire analysis was performed using VDJTools (). For repertoire overlap, similarity was measured as the clonotype-wise sum of the geometric mean frequencies and calculated as:F2ij=∑k=1Nφikφjk,where φik and φjk are the frequencies of clo […]

library_books

Three distinct developmental pathways for adaptive and two IFN γ producing γδ T subsets in adult thymus

2017
Nat Commun
PMCID: 5715069
PMID: 29203769
DOI: 10.1038/s41467-017-01963-w

[…] st TCR genes allowing insertions and gaps using miXCR software with settings optimised for RNA-Seq libraries including two assemblePartial and one extendAlignments runs, as recommended by the manual. VDJtools was used to eliminate erroneous clonotypes, filter for functionally recombined CDR3 sequences (by removing out-of-frame transcripts) and reduce the number of reads from each library to equal […]

library_books

Immune Repertoire after Immunization As Seen by Next Generation Sequencing and Proteomics

2017
Front Immunol
PMCID: 5650670
PMID: 29085363
DOI: 10.3389/fimmu.2017.01286

[…] used except a minimum UMI count of 1 in MIGEC. The resulting sequences were annotated for germline alleles and regions with the High-VQuest service (), and additional analysis was performed with the VDJTools package () for clustering of samples and tcR () to enumerate sequences overlapping between samples. VDJTools clustering was performed with the ClusterSamples function using the default distan […]

Citations

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VDJtools institution(s)
Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
VDJtools funding source(s)
The Russian Science Foundation project №14-14-00533 (VDJtools development) and RFBR grant 13-04-00998 (cDNA libraries preparation).

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