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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

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Publication for VDJ

VDJ in publications

 (6)
PMCID: 4981401
PMID: 27513338
DOI: 10.1371/journal.pone.0160853

[…] j segments (combinatorial diversity), and the insertion of non-templated (n) and palindromic nucleotides (p) at the junctions between v/d and d/j segments (junctional diversity). productive in-frame vdj rearrangements result in a functional heavy chain and lead to a permanent alteration of the genomic dna sequence of a b cell, defining it as a clone. similarly, the human immunoglobulin light […]

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

[…] reads., 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 […]

PMCID: 4795664
PMID: 26998518
DOI: 10.1126/sciadv.1501371

[…] 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 […]

PMCID: 4839220
PMID: 26802217
DOI: 10.1093/molbev/msw015

[…] 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 […]

PMCID: 4528417
PMID: 26194754
DOI: 10.1098/rstb.2014.0240

[…] the output. we also used vdjalign (http://github.com/cmccoy/ighutil), a simple smith–waterman alignment-based program previously used in an evolutionary analysis of immunoglobulin repertoires [], vdj (http://github.com/laserson/vdj), as used in [] and cloanalyst (v. 2015/1), a model-based approach using algorithms described in []. with the exception of vdj and vdjalign, which used a larger […]


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

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