VDJSeq-Solver – in Silico VDJ Recombination Detection tool

VDJSeq-Solver

:: DESCRIPTION

VDJSeq-Solver is a completely automated workflow for the in silico detection of the main clone V(D)J recombination sequence characterizing neoplastic tissues, using RNA-Seq paired-end reads.

::DEVELOPER

EDA (Electronic Design Automation Group)

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
TopHat
Java
Perl
BEDTools
Bowtie
Blast
SHRiMP
Samtools

:: DOWNLOAD

VDJSeq-Solver

:: MORE INFORMATION

Citation

VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool.
Paciello G, Acquaviva A, Pighi C, Ferrarini A, Macii E, Zamo’ A, Ficarra E.
PLoS One. 2015 Mar 23;10(3):e0118192. doi: 10.1371/journal.pone.0118192.

HTJoinSolver 0.4A – Human Immunoglobulin VDJ Partitioning

HTJoinSolver 0.4A

:: DESCRIPTION

HTJoinSolver is a pubically available application to assist researchers in partitioning the V(D)J regions of immunogloblulin.

::DEVELOPER

the Office of Intramural Research, Center for Information Technology in collaboration with the Vaccine Research Center at the National Institute of Allergy and Infectious Diseases.

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
JRE

:: DOWNLOAD

HTJoinSolver

:: MORE INFORMATION

Citation

HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs.
Russ DE, Ho KY, Longo NS.
BMC Bioinformatics. 2015 May 23;16(1):170. doi: 10.1186/s12859-015-0589-x.

Vidjil 201806 – High-throughput V(D)J Repertoire Analysis

Vidjil 201806

:: DESCRIPTION

Vidjil processes high-throughput sequencing data to extract V(D)J junctions and gather them into clones. This analysis is based on a seed heuristics and is fast and scalable, as, in the first phase, no alignment is performed with database germline sequences.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

Vidjil

:: MORE INFORMATION

Citation

Mathieu Giraud, Mikaël Salson, Marc Duez, Céline Villenet, Sabine Quief, Aurélie Caillault, Nathalie Grardel, Christophe Roumier, Claude Preudhomme, Martin Figeac,
Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing,
BMC Genomics, 15:409, doi:10.1186/1471-2164-15-409

VDJsolver 1.0b – Analysis of Human Immunoglobulin VDJ Recombination

VDJsolver 1.0b

:: DESCRIPTION

VDJsolver is a program that analyses human immunoglobulin VDJ recombination. The indetification of V and J genes is performed using standard sequencial alignment against databases of functional VH and JH genes from the IMGT database

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

VDJsolver

:: MORE INFORMATION

Citation

No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements.
Ohm-Laursen L, Nielsen M, Larsen SR, and Barington T.
Immunology. 119(2):265-77. 2006