Introduction

Change-O is a collection of tools for analyzing immunoglobulin sequences.

Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of immunoglobulin (Ig) repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of T and B lymphocytes. Change-O is a suite of utilities to handle advanced analysis of Ig sequences following germline segment assignment. Change-O handles output from IMGT/High V-quest and works off of a tab-delimited database file. It includes features for creating a personalized genotype, identifying sequences that are from a single B cell clone and inferring its lineage tree, analyzing amino acid properties, calculating diversity, generating a model of somatic hypermutation, and quantifying selection pressure. Record sorting, grouping, and sampling operations are also included.

Change-O Utilities

• Commandline Tools
  The Change-O commandline tools provide a set of utilities for automated processing of Ig repertoire data following germline segment assignment using a tools such as IMGT/HighV-QUEST.
  • AnalyzeAa
    Analyzes amino acid properties of the CDR3 region.
  • CreateGermlines
    Reconstructs germline sequences from alignment information.
  • DefineClones
    Assign Ig sequences into clonal groups.
  • GapRecords
    Multiple align groups of sequence records.
  • MakeDb
    Parses germline alignment output from IMGT/HighV-QUEST into a tab-delimited database file for import into other Change-O tools.
  • ParseDb
    Performs basic database operations on tab-delimited files.
• alakazam R package
  
  • Infers maximum parsimony lineage trees for clonal groups.
  • Calculates repertoire-level clonal diversity statistics.
• shazam R package
  
  • Calculates nearest neighbor distances for all sequences in a dataset.
  • Generates SHM mutability and substitution profiles.
  • Performs Bayesian estimation of antigen-driven selection.
• tigger R package
  
  • Infers an individual germline genotype from repertoire data.
  • Identifies novel V-region polymorphisms.

Citation

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.
Gupta NT*, Vander Heiden JA*, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH.
Bioinformatics 2015; doi: 10.1093/bioinformatics/btv359

Additional Ig Repertoire Tools & Component Pages

• pRESTO
  Raw read processing, assembly and annotation toolkit.
  
• BASELINe
  Bayesian estimation of antigen-driven selection.
  
• TIgGER
  Personal genotyping assignment and novel polymorphism detection.
  
• S5F
  A 5-mer microsequence context model of somatic hypermutation targeting and substitution rates.