Overview

Change-O performs analyses of lymphocyte receptor sequences following alignment against the germline reference. It includes tools for standardizing the output of alignment software, clonal assignment, germline reconstruction, and basic database manipulation. Change-O was designed to be simple to use, but it does require some familiarity with commandline applications. To maximize flexibility, Change-O employs a simple tab-delimited database format with standardized column names, allowing easy use of Change-O output with external environments and interoperability with the Alakazam, SHazaM, and TIgGER R packages. A brief description of each tool is shown in the table below.

Tool	Subcommand	Description
AlignRecords		Multiple aligns sequences in a database
	across	Aligns sequence columns within groups and across rows
	within	Aligns sequence fields within rows
	block	Aligns sequence groups across both columns and rows
AssignGenes	igblast	Runs IgBLAST on a fasta file
ConvertDb		Converts tab delimited database files
	airr	Converts input to an AIRR TSV file
	changeo	Converts input into a Change-O TSV file
	fasta	Creates a fasta file from database records
	baseline	Creates a special BASELINe formatted fasta file from a database
	genbank	Creates fasta and feature table files for input to tbl2asn
CreateGermlines		Reconstructs germline sequences from alignment data
DefineClones		Assigns clones by V gene, J gene and junction distance
MakeDb		Creates standardized databases from germline alignment results
	imgt	Parses IMGT/HighV-QUEST output
	igblast	Parses IgBLAST output and adds IMGT-gapping to the V-segment
	ihmm	Parses iHMMune-Align output
ParseDb		Parses annotations in tab delimited database files
	add	Adds fields to the database
	delete	Deletes specific records
	drop	Deletes entire fields
	index	Adds a numeric index field
	rename	Renames fields
	select	Selects specific records
	sort	Sorts records by a field
	update	Updates field and value pairs
	merge	Merge files
	split	Splits database files by field values