Repertoire sequencing data analysis bioinformatics software tools
The immunological repertoire is the collection of trans-membrane antigen-receptor proteins located on the surface of T and B cells. Repertoire sequencing (Rep-seq) has transformed the field of antigen receptor diversity studies, enabling deep and quantitative analysis for…
Desktop app
G T A T C G C T A MiTCR MiTCR

MiTCR

An open source software package aimed at extraction of information on…

An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data.

Desktop app
Web app
G T A T C G C T A IMGT/V-QUEST IMGT/V-QUEST

IMGT/V-QUEST

Identifies the variable (V), diversity (D) and joining (J) genes and alleles by…

Identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory.

Desktop app
G T A T C G C T A VDJFasta VDJFasta

VDJFasta

Bioinformatics Perl extension for the analysis of antibody variable domain…

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Desktop app
G T A T C G C T A Decombinator Decombinator

Decombinator

A tool for the fast, efficient analysis of T cell receptor (TcR) repertoire…

A tool for the fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience.

Desktop app
G T A T C G C T A partis partis

partis

An HMM-based framework for B-cell receptor sequence annotation, simulation, and…

An HMM-based framework for B-cell receptor sequence annotation, simulation, and clonal family inference. partis is especially effective for modern large sequencing data sets because it can infer…

Web app
G T A T C G C T A VDJServer VDJServer

VDJServer VDJServer

Provides immunology researchers with powerful data analysis infrastructure.…

Provides immunology researchers with powerful data analysis infrastructure. VDJserver offers tools for performing immune repertoire analysis with a focus on collaboration, streamlined metadata…

G T A T C G C T A TRIgS TRIgS

TRIgS

A collection of tools for downstream analysis of Rep-Seq data, including…

A collection of tools for downstream analysis of Rep-Seq data, including clustering and phylogenetic analysis. TRigS assists with the determination and analysis of B-cell lineage trees from…

Desktop app
G T A T C G C T A HTJoinSolver HTJoinSolver

HTJoinSolver

A V-(D)-J partitioning GUI application powered by novel approximate dynamic…

A V-(D)-J partitioning GUI application powered by novel approximate dynamic programming method that uses conserved immunoglobulin gene motifs to improve performance of aligning V-segments of…

Desktop app
G T A T C G C T A tcR tcR

tcR

A platform designed for TCR repertoire data analysis in R after preprocessing…

A platform designed for TCR repertoire data analysis in R after preprocessing data with MiTCR or other CDR3 extraction and gene alignment software tools. With the power and flexibility of R language…

Desktop app
G T A T C G C T A VDJtools VDJtools

VDJtools

A complementary software suite that solves a wide range of RepSeq post-analysis…

A complementary software suite that solves a wide range of RepSeq post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. The…

Desktop app
G T A T C G C T A VDJMLpy VDJMLpy

VDJMLpy

A standardized file format for representing V(D)J analysis results. VDJML…

A standardized file format for representing V(D)J analysis results. VDJML facilitates downstream processing of the results in an application-agnostic manner. The VDJML file format specification is…

Desktop app
G T A T C G C T A ARResT/Interrogate ARResT/Interrogate

ARResT/Interrogate

A web-based, interactive application for the analysis of immunoglobulins and T…

A web-based, interactive application for the analysis of immunoglobulins and T cell receptors using next-generation sequencing data. ARResT/Interrogate can organize and filter large amounts of…

Desktop app
G T A T C G C T A ImmuneDB ImmuneDB

ImmuneDB

A system for analyzing vast amounts of IGHV sequences and exploring the…

A system for analyzing vast amounts of IGHV sequences and exploring the resulting data. ImmuneDB can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well…

Desktop app
G T A T C G C T A Recover TCR Recover TCR

RTCR Recover TCR

A pipeline that accurately recovers T cell receptor (TCR) sequences, including…

A pipeline that accurately recovers T cell receptor (TCR) sequences, including rare TCR sequences, from high throughput sequencing data (including barcoded data) even at low coverage. RTCR employs a…

Desktop app
G T A T C G C T A VDJPuzzle VDJPuzzle

VDJPuzzle

A method to reconstruct the native TCRαβ from single cell RNA-seq data of…

A method to reconstruct the native TCRαβ from single cell RNA-seq data of Ag-specific T cells and then to link these with the gene expression profile of individual cells. The workflow allows…

Desktop app
G T A T C G C T A TraCeR TraCeR

TraCeR

A computational method to reconstruct full-length, paired T cell receptor (TCR)…

A computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by…

Desktop app
G T A T C G C T A repgenHMM repgenHMM

repgenHMM

A dynamic programming approach to learn the distribution of rearrangement…

A dynamic programming approach to learn the distribution of rearrangement scenarios from large numbers of non-productive sequences in an efficient way. This approach is based on a Hidden Markov…

Desktop app
G T A T C G C T A sciReptor sciReptor

sciReptor

A flexible toolkit for the processing and analysis of antigen receptor…

A flexible toolkit for the processing and analysis of antigen receptor repertoire sequencing data at single-cell level. The software combines bioinformatics tools for immunoglobulin sequence…

Desktop app
G T A T C G C T A clonotypeR clonotypeR

clonotypeR

A software package to identify and analyze antigen receptors from…

A software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the…

Desktop app
G T A T C G C T A LymAnalyzer LymAnalyzer

LymAnalyzer

A software package that significantly improves the completeness and accuracy of…

A software package that significantly improves the completeness and accuracy of TCR/IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. The…

Desktop app
G T A T C G C T A IMonitor IMonitor

IMonitor

Utilizes re-alignment to identify V(D)J genes and alleles after common local…

Utilizes re-alignment to identify V(D)J genes and alleles after common local alignment. A methodology is developed to correct the PCR and sequencing errors, and to minimize the PCR bias among various…

Desktop app
G T A T C G C T A IMmunEXplorer IMmunEXplorer

IMEX IMmunEXplorer

A user-friendly tool for analyzing and visualizing IG and TR repertoires based…

A user-friendly tool for analyzing and visualizing IG and TR repertoires based on NGS data. IMEX offers several algorithms for analyzing the clonality and diversity on multiple levels such as V-(D)-J…

Desktop app
G T A T C G C T A IgRepertoireConstructor

IgRepertoireConstructor

Performs error-correction of immunosequencing reads and uses mass spectra to…

Performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. IgRepertoireConstructor takes Illumina MiSeq paired end reads as an input…

Desktop app
Web app
G T A T C G C T A Bayesian estimation… Bayesian estimation of Antigen-driven SELectIoN

BASELINe Bayesian estimation of Antigen-driven SELectIoN

A computational framework for Bayesian estimation of antigen-driven selection…

A computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin sequences based on the analysis of somatic mutation patterns. BASELINe represents a fundamental advance…

Desktop app
G T A T C G C T A Change-O Change-O

Change-O

A suite of utilities which provides tools for advanced analyses of large-scale…

A suite of utilities which provides tools for advanced analyses of large-scale Ig repertoire sequencing data. Change-O includes tools for determining the complete set of Ig variable region gene…

Desktop app
G T A T C G C T A MiXCR MiXCR

MiXCR

A universal framework that processes big immunome data from raw sequences to…

A universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR…

Desktop app
G T A T C G C T A IgSimulator IgSimulator

IgSimulator

Simulating antibody repertoires is often the only feasible way to benchmark new…

Simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools. IgSimulator tool addresses various complications in generating realistic antibody repertoires.…

Desktop app
G T A T C G C T A IMmunogenetic… IMmunogenetic SEQuence Analysis

IMSEQ IMmunogenetic SEQuence Analysis

A method to derive clonotype repertoires from next generation sequencing data…

A method to derive clonotype repertoires from next generation sequencing data with sophisticated routines for handling errors stemming from PCR and sequencing artefacts. The application can handle…

Desktop app
G T A T C G C T A ImmunediveRsity ImmunediveRsity

ImmunediveRsity

A stand-alone pipeline primarily based in R programming for the integral…

A stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform…

Desktop app
G T A T C G C T A VDJSeq-Solver VDJSeq-Solver

VDJSeq-Solver

A pipeline to identify clonal lymphocyte populations from paired-end RNA…

A pipeline to identify clonal lymphocyte populations from paired-end RNA sequencing reads, with a primary focus on sequencing mRNA from neoplastic cells. VDJSeq-Solver detects the main clone for the…

Desktop app
G T A T C G C T A TIgGER TIgGER

TIgGER

Analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles,…

Analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This…

Web app
G T A T C G C T A ImmunoGlobulin Galaxy ImmunoGlobulin Galaxy

IGGalaxy ImmunoGlobulin Galaxy

A convenient web based application for analyzing next-generation sequencing…

A convenient web based application for analyzing next-generation sequencing results and reporting IGH gene rearrangements for both repertoire and clonality studies. IGGalaxy has two analysis options…

Desktop app
G T A T C G C T A TCRklass TCRklass

TCRklass

Identifies variable (V) and joining (J) segments, as well as CDR3 region…

Identifies variable (V) and joining (J) segments, as well as CDR3 region sequences using K-string-based algorithm for translated nucleotide queries. Specifically designed to handle short reads, the…

Desktop app
Web app
G T A T C G C T A IgBLAST IgBLAST

IgBLAST

Searches for germline variable (V), diversity (D) and joining (J) genes matches…

Searches for germline variable (V), diversity (D) and joining (J) genes matches for T-cell receptor (TCR) and immunoglobulin (IG) sequences using BLAST algorithm. Works both with amino-acid and…

Web app
G T A T C G C T A Vidjil Vidjil

Vidjil

Extracts clones from raw sequencing data and provides a web viewer to track…

Extracts clones from raw sequencing data and provides a web viewer to track lymphocyte populations along the time.

Desktop app
G T A T C G C T A VDJ VDJ

VDJ

A set of tools for profiling the human antibody repertoire.

A set of tools for profiling the human antibody repertoire.

Desktop app
G T A T C G C T A AbMining ToolBox AbMining ToolBox

AbMining ToolBox

These are python scripts to analyze antibody libraries sequenced by next…

These are python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).

Desktop app
G T A T C G C T A Molecular Identifier… Molecular Identifier Groups-based Error Correction

MiGEC Molecular Identifier Groups-based Error Correction

A cross-platform software pipeline that allows comprehensive processing of…

A cross-platform software pipeline that allows comprehensive processing of immune repertoire sequencing data, specifically focused on molecular barcoding for molecule counting and error correction.

Desktop app
G T A T C G C T A pRESTO pRESTO

pRESTO

A toolkit for processing raw reads from high-throughput sequencing of…

A toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.

Web app
Desktop app
G T A T C G C T A VDJviz VDJviz

VDJviz

A web-based graphical user interface application that allows browsing and…

A web-based graphical user interface application that allows browsing and analyzing immune repertoire sequencing (RepSeq) data. VDJviz can be used to visualize results of MITCR, MIGEC, MIXCR and…

Curators for Rep-seq analysis

  • Mikhail Shugay's avatar image
    Mikhail Shugay
    Genomics of Adaptive Immunity Lab,…
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