OverviewΒΆ

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

block

Aligns sequence groups across both columns and rows

within

Aligns sequence fields within rows

AssignGenes

igblast

Runs IgBLAST on a fasta file

ConvertDb

Converts tab delimited database files

airr

Converts input to an AIRR TSV file

baseline

Creates a special BASELINe formatted fasta file from a database

changeo

Converts input into a Change-O TSV file

fasta

Creates a fasta file from database records

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

igblast

Parses IgBLAST output and adds IMGT-gapping to the V-segment

ihmm

Parses iHMMune-Align output

imgt

Parses IMGT/HighV-QUEST 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

merge

Merge files

rename

Renames fields

select

Selects specific records

sort

Sorts records by a field

split

Splits database files by field values

update

Updates field and value pairs