O - Repertoire clonal assignment toolkit — changeo 1.3.3-2025.05.15 documentation (original) (raw)

Attention

As of v1.0.0 the default file format will be theAdaptive Immune Receptor Repertoire (AIRR) Community Rearrangement standard. The legacy Change-O format will still be supported through the --format changeoargument. See the Release Notes for more details.

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.

**IMPORTANT!**Active development of Change-O has moved to https://github.com/immcantation/changeo

Getting Started

• Overview
• Download
• Installation
• Data Standards
• Release Notes

Usage Documentation

• Commandline Usage
• API

Examples

• Using IgBLAST
• Parsing IMGT output
• Parsing 10X Genomics V(D)J data
• Filtering records
• Clustering sequences into clonal groups
• Reconstructing germline sequences
• Generating MiAIRR compliant GenBank/TLS submissions

Methods

• Clonal clustering methods
• Reconstruction of germline sequences from alignment data

About

• Contact
• Citation
• License

Indices

• Index
• Module Index