scholarly journals The pipeline repertoire of Ig-Seq analysis

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.

scholarly journals The pipeline repertoire of Ig-Seq analysis

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.

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

2017 ◽  
Vol 18 (1) ◽  
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

scholarly journals High-throughput immune repertoire analysis with IGoR

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Quentin Marcou ◽  
Thierry Mora ◽  
Aleksandra M. Walczak
Keyword(s):  
High Throughput ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Immune Repertoire Analysis

scholarly journals Best practices in metabarcoding of fungi: from experimental design to results

2021 ◽  
Author(s):  
Leho Tedersoo ◽  
Mohammad Bahram ◽  
Lucie Zinger ◽  
Henrik Nilsson ◽  
Peter Kennedy ◽  
...  
Keyword(s):  
Experimental Design ◽  
Best Practices ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Communities ◽  
Sequence Variants ◽  
Transcriptomic Data ◽  
Operational Taxonomic Units ◽  
Computational Analyses

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By re-analysing published datasets, we find that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, which is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared with the ITS2 subregion. We conclude that metabarcoding analyses of fungi are especially promising for co-analyses with the functional metagenomic or transcriptomic data, integrating fungi in the entire microbiome, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

scholarly journals IGoR: a tool for high-throughput immune repertoire analysis

2017 ◽  
Author(s):  
Quentin Marcou ◽  
Thierry Mora ◽  
Aleksandra M. Walczak
Keyword(s):  
T Cell ◽  
B Cells ◽  
High Throughput ◽  
T Cell Receptors ◽  
Diagnostic Tools ◽  
Biological Complexity ◽  
Immune Repertoire ◽  
Repertoire Analysis ◽  
Repertoire Sequencing ◽  
Immune Repertoire Analysis

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.

Scalable Sequence Clustering for Large-Scale Immune Repertoire Analysis

2021 ◽  
Author(s):  
Prem Bhusal ◽  
A K M Mubashwir Alam ◽  
Keke Chen ◽  
Ning Jiang ◽  
Jun Xiao
Keyword(s):  
Large Scale ◽  
Immune Repertoire ◽  
Sequence Clustering ◽  
Repertoire Analysis ◽  
Immune Repertoire Analysis
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