title: Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template.
abstract: BACKGROUND
  Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. The introduction of high throughput sequencing has generated unprecedented amounts of repertoire and mutation data from immunoglobulin genes. However, common analysis programs are not appropriate for pre-processing and analyzing these data due to the lack of a template or reference for the whole gene.
  
  
  RESULTS
  We present here the automated analysis pipeline we created for this purpose, which integrates various software packages of our own development and others', and demonstrate its performance.
  
  
  CONCLUSIONS
  Our analysis pipeline presented here is highly modular, and makes it possible to analyze the data resulting from high-throughput sequencing of immunoglobulin genes, in spite of the lack of a template gene. An executable version of the Automation program (and its source code) is freely available for downloading from our website: http://immsilico2.lnx.biu.ac.il/Software.html.
authors: The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel. Ramit.Mehr@BIU.ac.il.
authors: Miri
authors: M
authors: Michaeli
authors: Michal
authors: M
authors: Barak
authors: Lena
authors: L
authors: Hazanov
authors: Hila
authors: H
authors: Noga
authors: Ramit
authors: R
authors: Mehr
references: Trends Immunol. 2009 Apr;30(4):173-81
references: 19303358
references: Bioinformatics. 2006 Feb 15;22(4):438-44
references: 16357034
references: Nature. 2009 Apr 2;458(7238):636-40
references: 19287373
references: Int Immunol. 2008 May;20(5):683-94
references: 18397909
references: Front Immunol. 2012 Dec 28;3:386
references: 23293637
references: Bioinformatics. 2007 Jul 1;23(13):1580-7
references: 17463026
references: Mol Immunol. 2009 Jan;46(3):305-20
references: 19062097
references: Eur J Immunol. 2010 Apr;40(4):1150-61
references: 20104489
references: Aging Cell. 2011 Dec;10(6):922-30
references: 21726404
references: Immunogenetics. 2012 May;64(5):337-50
references: 22200891
references: Sci Transl Med. 2009 Dec 23;1(12):12ra23
references: 20161664
references: J Autoimmun. 2010 Dec;35(4):325-35
references: 20727711
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504
references: 21665923
references: J Immunol. 2010 Jun 15;184(12):6986-92
references: 20495067
references: Immunol Lett. 2012 Nov-Dec;148(1):11-22
references: 22902400
references: Dev Immunol. 2002 Dec;9(4):233-43
references: 15144020
references: Science. 2009 May 8;324(5928):807-10
references: 19423829
references: Bioinformatics. 2007 Nov 1;23(21):2947-8
references: 17846036
references: Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13081-6
references: 18723673
references: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W503-8
references: 18503082
references: Blood. 2010 Aug 19;116(7):1070-8
references: 20457872
references: J Immunol Methods. 2008 Sep 30;338(1-2):67-74
references: 18706908
references: Int Immunol. 2010 Nov;22(11):875-87
references: 21059768