title: ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.
abstract: BACKGROUND
  Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background. To facilitate the analysis of T and B cell repertoires by less experienced users, software is needed that combines the most common tools for repertoire analysis.
  
  
  RESULTS
  We introduce a graphical user interface (GUI) providing a complete analysis pipeline for processing raw NGS data for human and animal TCR and BCR clonotype determination and advanced differential repertoire studies. It provides two applications. ClonoCalc prepares the raw data for downstream analyses. It combines a demultiplexer for barcode splitting and employs MiXCR for paired-end read merging and the extraction of human and animal TCR/BCR sequences. ClonoPlot wraps the R package tcR and further contributes self-developed plots for the descriptive comparative investigation of immune repertoires.
  
  
  CONCLUSIONS
  This workflow reduces the amount of programming required to perform the respective analyses and supports both communication and training between scientists and technicians, and across scientific disciplines. The Open Source development in Java and R is modular and invites advanced users to extend its functionality. Software and documentation are freely available at https://bitbucket.org/ClonoSuite/clonocalc-plot .
authors.affiliation: Institute of Anatomy, Ratzeburger Allee, Lübeck, 160, 23562, Germany. faehnrich@anat.uni-luebeck.de.
authors.forename: Anke
authors.initials: A
authors.lastname: Fähnrich
authors.affiliation: Institute for Software Engineering and Programming Languages, Ratzeburger Allee, Lübeck, 160, 23562, Germany.
authors.forename: Moritz
authors.initials: M
authors.lastname: Krebbel
authors.affiliation: Institute for Software Engineering and Programming Languages, Ratzeburger Allee, Lübeck, 160, 23562, Germany.
authors.forename: Normann
authors.initials: N
authors.lastname: Decker
authors.affiliation: Institute for Software Engineering and Programming Languages, Ratzeburger Allee, Lübeck, 160, 23562, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Leucker
authors.affiliation: Institute for Software Engineering and Programming Languages, Ratzeburger Allee, Lübeck, 160, 23562, Germany.
authors.forename: Felix D
authors.initials: FD
authors.lastname: Lange
authors.affiliation: Institute of Anatomy, Ratzeburger Allee, Lübeck, 160, 23562, Germany.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Kalies
authors.affiliation: Institute for Biostatistics and Informatics in Medicine and Ageing Research, Ernst-Heydemann-Str. 8, Rostock, 18057, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Möller
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D011947:Receptors, Antigen, B-Cell / Q000276:immunology* / Q000378:metabolism; D011948:Receptors, Antigen, T-Cell / Q000276:immunology* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
chemical_list: D011947:Receptors, Antigen, B-Cell; D011948:Receptors, Antigen, T-Cell
keywords: Graphical user interface; Immune repertoire analysis; Next-generation sequencing