Attention

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

https://img.shields.io/pypi/dm/changeo https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic

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.

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

To update Git configuration settings:

git config user.email “your-gh-user@email.com

git config user.name “your-gh-user-name”

git remote set-url origin git@github.com:immcantation/changeo.git

Usage Documentation

Indices