MiXCR 3.0.13 – Analysis of T- and B- cell Receptor Repertoire Sequencing data

MiXCR 3.0.13

:: DESCRIPTION

MiXCR is an universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

::DEVELOPER

MiLaboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JRE
:: DOWNLOAD

 MiXCR

:: MORE INFORMATION

Citation:

Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364.
MiXCR: software for comprehensive adaptive immunity profiling.
Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M3, Mamedov IZ, Putintseva EV, Chudakov DM.

Y-Tools 3.1.1 – Construction of Antibody Repertoire and Immunoproteogenomics Analysis

Y-Tools 3.1.1

:: DESCRIPTION

Y-Tools are tools for construction of full-length adaptive immune repertoires and immunoinformatics analysis

::DEVELOPER

Algorithmic Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Y-Tools

:: MORE INFORMATION

Citation

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.
Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA.
Bioinformatics. 2015 Jun 15;31(12):i53-i61. doi: 10.1093/bioinformatics/btv238.

BRepertoire – Analysing Antibody Repertoire Data

BRepertoire

:: DESCRIPTION

BRepertoire is a suite of user-friendly web-based software tools for large-scale statistical analyses of antibody repertoire data. It works on data preprocessed by IMGT, and performs statistical and comparative analyses on-the-fly with versatile plotting options.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Margreitter C, Lu HC, Townsend C, Stewart A, Dunn-Walters DK, Fraternali F.
BRepertoire: a user-friendly web server for analysing antibody repertoire data.
Nucleic Acids Res. 2018 Jul 2;46(W1):W264-W270. doi: 10.1093/nar/gky276. PMID: 29668996; PMCID: PMC6031031.

LymAnalyzer 1.2.2 – Analysis TCR/IG Repertoire from High-throughput Sequencing reads

LymAnalyzer 1.2.2

:: DESCRIPTION

LymAnalyzer is a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.

::DEVELOPER

LymAnalyzer team

:: SCREENSHOTS

lymanalyzer

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Java

:: DOWNLOAD

 LymAnalyzer

:: MORE INFORMATION

Citation:

LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.
Yu Y, Ceredig R, Seoighe C.
Nucleic Acids Res. 2015 Oct 7. pii: gkv1016.

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

tcR 2.2.4 – T Cell Receptor Repertoire Advanced data analysis

tcR 2.2.4

:: DESCRIPTION

tcR is a platform designed for TCR repertoire data analysis in R after preprocessing data with CDR3 extraction and gene alignment software tools such as MiTCR, ImmunoSEQ and MiGEC.

::DEVELOPER

Laboratory of Comparative and Functional Genomic

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

 tcR

:: MORE INFORMATION

Citation:

tcR: an R package for T cell receptor repertoire advanced data analysis.
Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Lebedev YB, Mamedov IZ.
BMC Bioinformatics. 2015 May 28;16:175. doi: 10.1186/s12859-015-0613-1.

VDJtools 1.2.1 – Post-analysis of Immune Repertoire Sequencing data

VDJtools 1.2.1

:: DESCRIPTION

VDJtools is a comprehensive framework for post-analysis of immune repertoire sequencing data.

::DEVELOPER

Immuno-sequencing Algorithms Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • JRE
:: DOWNLOAD

 VDJtools

:: MORE INFORMATION

Citation:

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM.
PLoS Comput Biol. 2015 Nov 25;11(11):e1004503. doi: 10.1371/journal.pcbi.1004503.

IgSimulator – Versatile tool for Simulation of Immunoglobulin Repertoire

IgSimulator

:: DESCRIPTION

IgSimulator is a tool for simulation of antibody repertoire and Ig-seq library. IgSimulator is designed for testing and benchmarking tools for reconstruction of Ig repertoires.

::DEVELOPER

Yana Safonova (Center for Algorithmic Biotechnology, Saint Petersburg State University).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 IgSimulator

:: MORE INFORMATION

Citation

IgSimulator: a versatile immunosequencing simulator.
Safonova Y, Lapidus A, Lill J.
Bioinformatics. 2015 May 25. pii: btv326.