High-throughput immune repertoire analysis with IGoR

High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of these datasets. We present IGoR - a new comprehensive tool that takes B or T-cell receptors sequence reads and quantitatively characterizes the statistics of receptor generation from both cDNA and gDNA. It probabilistically annotates sequences and its modular structure can investigate models of increasing biological complexity for different organisms. For B-cells IGoR returns the hypermutation statistics, which we use to reveal co-localization of hypermutations along the sequence. We demonstrate that IGoR outperforms existing tools in accuracy and estimate the sample sizes needed for reliable repertoire characterization.

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ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

BMC Bioinformatics ◽

10.1186/s12859-017-1575-2 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 11

Author(s):

Anke Fähnrich ◽

Moritz Krebbel ◽

Normann Decker ◽

Martin Leucker ◽

Felix D. Lange ◽

...

Keyword(s):

User Interface ◽

Graphical User Interface ◽

Immune Repertoire ◽

Repertoire Analysis ◽

Immune Repertoire Analysis

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The pipeline repertoire of Ig-Seq analysis

10.7287/peerj.preprints.27444 ◽

2018 ◽

Author(s):

Laura López-Santibáñez-Jácome ◽

Selma Eréndira Avendaño-Vázquez ◽

Carlos Fabián Flores-Jasso

Keyword(s):

Experimental Design ◽

High Throughput Sequencing ◽

Immune Repertoire ◽

Computational Tools ◽

Repertoire Analysis ◽

Strategic Approach ◽

Antibody Repertoires ◽

Computational Analyses ◽

Immune Repertoire Analysis

With the advent of high-throughput sequencing of immunoglobulins (Ig-Seq), the understanding of antibody repertoires and its dynamics among individuals and populations has become and exiting area of research. There are an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide an organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational analyses of immune repertoires.

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T and B Cell Receptor Immune Repertoire Analysis using Next-generation Sequencing

Journal of Visualized Experiments ◽

10.3791/61792 ◽

2021 ◽

Author(s):

Lael Werner ◽

Chen Dor ◽

Naomi Salamon ◽

Meital Nagar ◽

Dror S. Shouval

Keyword(s):

Next Generation Sequencing ◽

B Cell ◽

Cell Receptor ◽

B Cell Receptor ◽

Next Generation ◽

Immune Repertoire ◽

Repertoire Analysis ◽

Generation Sequencing ◽

Immune Repertoire Analysis

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The pipeline repertoire of Ig-Seq analysis

10.7287/peerj.preprints.27444v1 ◽

2018 ◽

Cited By ~ 2

Author(s):

Laura López-Santibáñez-Jácome ◽

Selma Eréndira Avendaño-Vázquez ◽

Carlos Fabián Flores-Jasso

Keyword(s):

Experimental Design ◽

High Throughput Sequencing ◽

Immune Repertoire ◽

Computational Tools ◽

Repertoire Analysis ◽

Strategic Approach ◽

Antibody Repertoires ◽

Computational Analyses ◽

Immune Repertoire Analysis

With the advent of high-throughput sequencing of immunoglobulins (Ig-Seq), the understanding of antibody repertoires and its dynamics among individuals and populations has become and exiting area of research. There are an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide an organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational analyses of immune repertoires.

Download Full-text