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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…
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MiTCR
Desktop

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.

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TraCeR
Desktop

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…

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MiXCR
Desktop

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…

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MiGEC
Desktop

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.

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Decombinator
Desktop

Decombinator

Allows users to analyze T-cell receptor (TCR) repertoire sequences produced by…

Allows users to analyze T-cell receptor (TCR) repertoire sequences produced by deep sequencing.

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partis
Desktop

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…

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IgDiscover
Desktop

IgDiscover

Identifies germline V genes from expressed repertoires to a specificity of…

Identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in…

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pRESTO
Desktop

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.

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LymAnalyzer
Desktop

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…

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AbSim
Desktop

AbSim

Enables the simulation of time-resolved antibody repertoires. AbSim is an R…

Enables the simulation of time-resolved antibody repertoires. AbSim is an R package that allows user to comprehensively control the vast biologically-relevant parameter space of antibody repertoire…

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ImmuneDB
Desktop

ImmuneDB

Analyzes vast amounts of IGHV (immunoglobulin heavy-chain variable) sequences…

Analyzes vast amounts of IGHV (immunoglobulin heavy-chain variable) sequences and exploring the resulting data. ImmuneDB can take as input raw FASTA/FASTQ data, identify genes, determine clones,…

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HTJoinSolver
Desktop
Web

HTJoinSolver

Handles alignments with insertions/deletions (indels), while maintaining or…

Handles alignments with insertions/deletions (indels), while maintaining or improving the speed. HTJOINSOLVER is a desktop application, provided as an implementation of the partitioning method.…

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ALPHABETR
Desktop

ALPHABETR ALgorithm for Pairing alPHA-BETa T cell Receptors

Implements algorithms for obtaining T cell receptors (TCR) sequence pairs.…

Implements algorithms for obtaining T cell receptors (TCR) sequence pairs. ALPHABETR determines CDR3A/CDR3B pairs from high-throughput sequencing data from repeated samples of antigen-specific T cell…

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VDJPuzzle
Desktop

VDJPuzzle

Allows users to reconstruct the native T-cell receptors (TCR)αβ from single…

Allows users to reconstruct the native T-cell receptors (TCR)αβ from single cell RNA-seq data of Ag-specific T cells and to link these with the gene expression profile of individual cells.…

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ImmunediveRsity
Desktop

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…

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VDJFasta
Desktop

VDJFasta

Bioinformatics Perl extension for the analysis of antibody variable domain…

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

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TRIgS
Desktop

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…

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ARResT/Interrog…
Desktop

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…

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RTCR
Desktop

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…

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repgenHMM
Desktop

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…

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IMPre
Desktop

IMPre Immune Germline Prediction

Involves data processing, clustering, assembly, and optimization. IMPre is a…

Involves data processing, clustering, assembly, and optimization. IMPre is a method that provides a comprehensive approach for identification of novel B- and T-cell receptor (BCR/TCR) genes and…

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SONAR
Desktop

SONAR Software for the Ontogenic aNalysis of Antibody Repertoires

Annotates next-generation sequencing data, identifies transcripts in a lineage…

Annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR is capable of automating both general…

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RDI
Desktop

RDI Repertoire Dissimilarity Index

Estimates the repertoire differences. RDI is a computational approach allowing…

Estimates the repertoire differences. RDI is a computational approach allowing comparison between different types of repertoires. It is useful for all analysis of immune sequences and it can be…

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ClonoPlot
Desktop

ClonoPlot

Contributes self-developed plots for the descriptive comparative investigation…

Contributes self-developed plots for the descriptive comparative investigation of immune repertoires. ClonoPlot allows the visualization of observations in comparative B cell receptors (BCR) and T…

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VDJviz
Web
Desktop

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…

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BASELINe
Desktop
Web

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…

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TCRbiter
Desktop

TCRbiter

Distinguishes T cell receptor (TCR) rearrangements from reads spanning the…

Distinguishes T cell receptor (TCR) rearrangements from reads spanning the remainder of the genome. It was tested against in silico simulations and real clinical data. It represents a method for…

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MaxSnippetModel
Desktop

MaxSnippetModel

Allows application of standard machine learning techniques to mine full set of…

Allows application of standard machine learning techniques to mine full set of repertoire sequences for sequence patterns. MaxSnippetModel scores every snippet by its biochemical features with a…

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IGoR
Desktop

IGoR Inference and Generation Of Repertoires

Processes raw immune sequence reads from any source and learns unbiased…

Processes raw immune sequence reads from any source and learns unbiased statistics of recombination and somatic hypermutations. IGoR is a flexible computational method that outputs a whole list of…

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IgRepertoireCon…
Desktop

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…

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Change-O
Desktop

Change-O

Provides a suite of utilities that cover a range of complex analysis tasks for…

Provides a suite of utilities that cover a range of complex analysis tasks for immunoglobulin (Ig) repertoire sequencing data. Change-O is a suite of utilities that (i) processes the output of V(D)J…

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IgSimulator
Desktop

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.…

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IMSEQ
Desktop

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…

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VDJMLpy
Desktop

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…

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TRIg
Desktop

TRIg T-cell receptor antibody

Aligns non-regular T-cell receptor and immunoglobulin sequences. TRIg does…

Aligns non-regular T-cell receptor and immunoglobulin sequences. TRIg does alignments to the whole receptor gene instead of only to the coding regions. This tool applies a heuristic strategy and…

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sciReptor
Desktop

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…

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TCRklass
Desktop

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…

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VDJtools
Desktop

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…

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IMonitor
Desktop

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…

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IgBLAST
Desktop
Web

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…

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VDJSeq-Solver
Desktop

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…

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tcR
Desktop

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…

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IMEX
Desktop

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…

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AbMining…
Desktop

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).

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Vidjil
Web

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.

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VDJServer
Web

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…

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clonotypeR
Desktop

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…

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TIgGER
Desktop

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…

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IGGalaxy
Web

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…

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VDJ
Desktop

VDJ

A set of tools for profiling the human antibody repertoire.

A set of tools for profiling the human antibody repertoire.

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alakazam
Desktop

alakazam

Provides methods to investigate lymphocyte receptor clonal lineages, diversity,…

Provides methods to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties. Alakazam was developed to (i) provides core functionality for R…

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LymphoSeq
Desktop

LymphoSeq

Allows analysis of high-throughput sequencing (HST) of T and B cell receptor…

Allows analysis of high-throughput sequencing (HST) of T and B cell receptor complementarity determining region 3 (CDR3) sequences. LymphoSeq performs multiple sequence alignment of all amino acid or…

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