As of v1.0.0 the default file format will be the
Adaptive Immune Receptor Repertoire (AIRR) Community Rearrangement standard.
The classical Change-O format will still be supported through the
argument. See the Release Notes for more details.
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.
- Using IgBLAST
- Parsing IMGT output
- Parsing 10X Genomics V(D)J data
- Filtering records
- Clustering sequences into clonal groups
- Reconstructing germline sequences
- IgPhyML lineage tree analysis
- Generating MiAIRR compliant GenBank/TLS submissions