Introduction

Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and somatic diversity of the Ig repertoire presents challenges for biologically meaningful analysis, which requires specialized computational methods. We have developed a suite of utilities, Change-O, which provides tools for advanced analyses of large-scale Ig repertoire sequencing data. Change-O includes tools for determining the complete set of Ig variable region gene segment alleles carried by an individual (including novel alleles), partitioning of Ig sequences into clonal populations, creating lineage trees, inferring somatic hypermutation targeting models, measuring repertoire diversity, quantifying selection pressure, and calculating sequence chemical properties. All Change-O tools utilize a common data format, which enables the seamless integration of multiple analyses into a single workflow.Change-O is freely available for non-commercial use and may be downloaded from http://clip.med.yale.edu/changeo.steven.kleinstein@yale.edu.

Publications

  1. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.
    Cite this
    Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH, 2015-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Namita T Gupta
    Developer

    Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, United States of America

  2. Jason A Vander Heiden
    Developer

    Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, United States of America

  3. Mohamed Uduman
    Developer

    Department of Pathology, Yale University School of Medicine, United States of America

  4. Daniel Gadala-Maria
    Developer

    Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, United States of America

  5. Gur Yaari
    Developer

    Bioengineering Program, Faculty of Engineering, Israel

  6. Steven H Kleinstein
    Investigator

    Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, United States of America

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Summary
AccessionBT006921
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted BySteven H Kleinstein