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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

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Documentation


Maintainer


  • person_outline Mikhail Shugay <>

Publication for VDJtools

VDJtools in publications

 (13)
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., the cdr3 sequence was defined as the amino acids between the second cysteine of the v region and the conserved phenylalanine of the j region, according to imgt. cdr3 sequences shown in tabl […]

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., data were analyzed using the graphpad prism version 6.0b and 4.0. to test for normal distribution of data, d’agostino and pearson […]

PMCID: 5826233
PMID: 29515587
DOI: 10.3389/fimmu.2018.00291

[…] 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., all continuous variables are presented as median values with interquartile range, unless […]

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

[…] 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 […]

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

[…] 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 […]


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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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