ArticleNucleic acids research2016
LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Comprehensive characterization of V(D)J recombination from long-read transcriptomic data with VDJcraft.bioRxiv : the preprint server for biology · 2026Article
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- Article
- Development and characterization of human T-cell receptor (TCR) alpha and beta clones' library as biological standards and resources for TCR sequencing and engineering.Biology methods & protocols · 2024Article
- AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets.Immunoinformatics (Amsterdam, Netherlands) · 2023Article
- T cell receptor beta germline variability is revealed by inference from repertoire data.Genome medicine · 2022Article
- Article
- Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2.Nature communications · 2021Article
- Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset.Frontiers in immunology · 2021Article
- Tools for fundamental analysis functions of TCR repertoires: a systematic comparison.Briefings in bioinformatics · 2020Article
- Best practices for bioinformatic characterization of neoantigens for clinical utility.Genome medicine · 2019Review
- The Pipeline Repertoire for Ig-Seq Analysis.Frontiers in immunology · 2019Review
- Cernunnos/Xlf Deficiency Results in Suboptimal V(D)J Recombination and Impaired Lymphoid Development in Mice.Frontiers in immunology · 2019Article
- Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information.Journal of immunology (Baltimore, Md. : 1950) · 2018Article
- CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling.Blood advances · 2018Article
- High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities.Briefings in bioinformatics · 2018Article
- PAXX and Xlf interplay revealed by impaired CNS development and immunodeficiency of double KO mice.Cell death and differentiation · 2018Article
- Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018Review
- Overview of methodologies for T-cell receptor repertoire analysis.BMC biotechnology · 2017Article
- ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.BMC bioinformatics · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The adaptive immune system includes populations of B and T cells capable of binding foreign epitopes via antigen specific receptors, called immunoglobulin (IG) for B cells and the T cell receptor (TCR) for T cells. In order to provide protection from a wide range of pathogens, these cells display highly diverse repertoires of IGs and TCRs. This is achieved through combinatorial rearrangement of multiple gene segments in addition, for B cells, to somatic hypermutation. Deep sequencing technologies have revolutionized analysis of the diversity of these repertoires; however, accurate TCR/IG diversity profiling requires specialist bioinformatics tools. Here we present LymAnalzyer, 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. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available. Implemented in Java, it includes both a command line version and a graphical user interface and is freely available at https://sourceforge.net/projects/lymanalyzer/.
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