Y-tools: a novel toolkit for analysis of antibody repertoires using immunosequencing data
Reconstruction and analysis of antibody repertoire is an important part of various immunological studies. While modern biotechnologies allow one to perform deep and full length scan of circulating antibodies using immunosequencing and mass spectrometry, there is no gold standard toolkit for their analysis. Here we present a novel multipurpose toolkit for construction and investigation of adaptive immune repertoires using immunosequencing and mass spectra data. It includes IgRepertoireConstructor , an algorithm for antibody repertoire construction and immunoproteogenomics analysis; AntEvolo, an algorithm for construction of clonal trees and evolutionary analysis of antibody repertoires; aimQUAST , a quality assessment tool for adaptive immune repertoires; and IgSimulator , a versatile simulator of antibody repertoire. IgRepertoireConstructor, IgSimulator and aimQUAST are freely available at Github. AntEvolo to be released in fall 2016.
 Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.Bioinformatics. 2015 Jun 15; 31(12): i53-61.
 Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Yana Safonova. New algorithmic challenges of adaptive immune repertoire construction. Paper accepted at the RECOMB-Seq 2016. doi: arXiv:1604.02193
 Safonova Y, Lapidus A, Lill J. IgSimulator: a versatile immunosequencing simulator. Bioinformatics. 2015 Oct 1; 31(19): 3213-5.