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|Interface||Command line interface, Graphical user interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
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- person_outline Cathal Seoighe
Publication for LymAnalyzer
Overview of methodologies for T cell receptor repertoire analysis
[…] data containing UMIs are MIGEC  and pRESTO . The tools listed above are mainly used for primary analysis, as the recovery of TCR sequences from raw data and successive clustering and annotation. LymAnalyzer additionally contains a feature for SNP calling and sequence mutation trees generation for IGs.Further (secondary) data analysis of the immune repertoire classically involves the calculati […]
3D: diversity, dynamics, differential testing – a proposed pipeline for analysis of next generation sequencing T cell repertoire data
[…] iversity and dynamics of the repertoire. For example, miXCR  is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. The more comprehensive software, LymAnalyzer , consists of four functional components: VDJ gene alignment, CDR3 extraction, polymorphism analysis and lineage mutation tree construction. sciReptor  is a flexible toolkit for the pr […]
High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease
[…] ew V–D–J gene annotation tools based on various algorithms are reported, such as IgBLAST (), iHMMune-align (), and Decombinator (, ) (Table ). In addition, many integrated bioinformatic tools (MiTCR, LymAnalyzer, Change-O, etc.) for data processing are developed recently (–) (Table ), which provides various statistical approaches for diversity estimation, repertoire comparison, clustering analysis […]
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