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
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
ParseDb   Parses tab delimited database files
  fasta Creates a fasta file from database records
  clip Creates a special BASELINe formatted fasta file from a database
  split Splits database files by field values
  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
DefineClones   Groups Ig sequences into clonal clusters
  bygroup Assigns clones by V-gene, J-gene and junction distance
  hclust Assigns clones by full sequences with gene mismatch penalities
CreateGermlines   Reconstructs germline sequences from alignment data