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Number of citations per year for the bioinformatics software tool VDJ
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Protocols

VDJ specifications

Information


Unique identifier OMICS_04064
Name VDJ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Publication for VDJ

VDJ citations

 (12)
library_books

Many Routes to an Antibody Heavy Chain CDR3: Necessary, Yet Insufficient, for Specific Binding

2018
Front Immunol
PMCID: 5852061
PMID: 29568296
DOI: 10.3389/fimmu.2018.00395

[…] 596,145 productive MiSeq reads comprising 7,984,053 unique HCDR3s from the naïve B cells of three donors, we identified 568 identical HCDR3s (0.007% of the total unique HCDR3s) generated by different VDJ recombinations (as determined by IMGT). These were generated using from two to 26 different VDJ combinations (see Table S1 in Supplementary Material), and 176 of these rearrangements were found in […]

library_books

High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease

2016
Front Immunol
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] and for tracking changes in clonal populations during the clinical course of infection. Several different methods may be used to describe the diversity of lymphocyte repertoires at different levels – VDJ recombination diversity (), Simpson diversity index (, ), and some non-parametric methods. Decrease in the overall diversity of the immune repertoire have been observed after various antigen expos […]

library_books

A Public Database of Memory and Naive B Cell Receptor Sequences

2016
PLoS One
PMCID: 4981401
PMID: 27513338
DOI: 10.1371/journal.pone.0160853

[…] this dataset enables access to to in this study, and each of them is followed by a set of interactive dashboards that allow viewing different aspects the data, such as Occupancy (data underlying ), VDJ tools (data underlying ), CDR3 tools (data underlying ), Substitutions tools (data underlying ), and SHM tools (data underlying ). Most dashboards include a sample selection option: data are coded […]

library_books

Statistical inference of a convergent antibody repertoire response to influenza vaccine

2016
Genome Med
PMCID: 4891843
PMID: 27255379
DOI: 10.1186/s13073-016-0314-z

[…] State-of-the-art tools for aligning RNA-seq reads to a reference genome, such as TopHat2 [], were not designed, and are ill-equipped, to handle the various eccentricities of Ab RNA (such as VDJ gene segment recombination, as well as the high number of mutations expected from both VDJ recombination and SHM). Similar to others [, ], we therefore developed a bioinformatic pipeline that will […]

library_books

Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting

2016
Sci Adv
PMCID: 4795664
PMID: 26998518
DOI: 10.1126/sciadv.1501371

[…] e used in the first-step singleplex PCR reaction (fig. S2B). CLC Genomics Workbench preprocessed sequences (370,000) were randomly input from each of the five replicate data sets and processed in our VDJ annotation and analysis pipeline (table S1). The number of unique RIDs for each spike-in clone was counted and converted into frequency (%) and then averaged to produce the singleplex PCR (or rela […]

library_books

The Diversity and Molecular Evolution of B Cell Receptors during Infection

2016
Mol Biol Evol
PMCID: 4839220
PMID: 26802217
DOI: 10.1093/molbev/msw015

[…] CR sequences poses challenges for targeted sequencing. We provide here only a brief summary of current sequencing approaches, in particular as they relate to the analysis of BCR diversity. Rearranged VDJ segments are flanked by introns, so targeting germline DNA requires a cocktail of polymerase chain reaction (PCR) primers (). A challenge for this approach is to control for PCR bias, which could […]


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VDJ institution(s)
Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA

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