Change-O - Repertoire clonal assignment toolkit

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.

Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of Ig repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of B cells and T cells. Change-O is a suite of utilities to facilitate advanced analysis of Ig and TCR sequences following germline segment assignment. Change-O handles output from IMGT/HighV-QUEST and IgBLAST, and provides a wide variety of clustering methods for assigning clonal groups to Ig sequences. Record sorting, grouping, and various database manipulation operations are also included.

Getting Started

• Overview
• Download
• Installation
  • Requirements
  • Linux
  • Mac OS X
  • Windows
• Data Standard

Examples

• Using IgBLAST
  • Example data
  • Configuring IgBLAST
  • Running IgBLAST
  • Processing the output of IgBLAST
• Parsing IMGT output
  • Example data
  • Reducing file size for submission to IMGT/HighV-QUEST
  • Processing the output of IMGT/HighV-QUEST
• Parsing 10X Genomics V(D)J data
  • Example data
  • Converting 10X V(D)J data into Change-O format
  • Joining Change-O data with 10X V(D)J annotations
  • Identifying clones from B cells in Change-O format 10X V(D)J data
• Filtering records
  • Removing non-functional sequences
  • Removing disagreements between the C-region primers and the reference alignment
  • Exporting records to FASTA files
• Clustering sequences into clonal groups
  • Example data
  • Determining a clustering threshold
  • Assigning clones
• Reconstructing germline sequences
  • Example data
  • Adding germline sequences to the database
• IgPhyML lineage tree analysis
  • Installation
  • Quick start
  • Processing Change-O data sets
• Generating MiAIRR compliant GenBank/TLS submissions
  • MiAIRR
  • Example data
  • Generating files for submission
  • Submitting to GenBank/TLS using SequinMacroSend

Methods

• Clonal clustering methods
  • Clustering by V-gene, J-gene and junction length
• Reconstruction of germline sequences from alignment data

Usage Documentation

• Commandline Usage
  • AlignRecords
  • AssignGenes
  • BuildTrees
  • ConvertDb
  • CreateGermlines
  • DefineClones
  • MakeDb
  • ParseDb
• API
  • changeo.Alignment
  • changeo.Applications
  • changeo.Commandline
  • changeo.Distance
  • changeo.Gene
  • changeo.IO
  • changeo.Multiprocessing
  • changeo.Receptor

About

• Release Notes
• Contact
• Citation
• License

Related Projects

• Immcantation Portal
• pRESTO
• Alakazam
• SHazaM
• TIgGER
• RDI

Indices

• Index
• Module Index