changeo
0.4.6

Getting Started

  • Overview
  • Download
  • Installation
  • Data Standard

Examples

  • 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

Methods

  • Clonal clustering methods
  • Reconstruction of germline sequences from alignment data

Usage Documentation

  • Commandline Usage
    • AlignRecords
    • AssignGenes
    • BuildTrees
    • ConvertDb
    • CreateGermlines
    • DefineClones
    • MakeDb
    • ParseDb
  • API

About

  • Release Notes
  • Contact
  • Citation
  • License

Related Projects

  • Immcantation Portal
  • pRESTO
  • Alakazam
  • SHazaM
  • TIgGER
  • RDI
changeo
  • Docs »
  • Commandline Usage
  • Edit on Bitbucket

Commandline UsageΒΆ

  • AlignRecords
    • AlignRecords across
    • AlignRecords block
    • AlignRecords within
  • AssignGenes
    • AssignGenes igblast
  • BuildTrees
  • ConvertDb
    • ConvertDb airr
    • ConvertDb baseline
    • ConvertDb changeo
    • ConvertDb fasta
    • ConvertDb genbank
  • CreateGermlines
  • DefineClones
  • MakeDb
    • MakeDb igblast
    • MakeDb ihmm
    • MakeDb imgt
  • ParseDb
    • ParseDb add
    • ParseDb delete
    • ParseDb drop
    • ParseDb index
    • ParseDb merge
    • ParseDb rename
    • ParseDb select
    • ParseDb sort
    • ParseDb split
    • ParseDb update
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© Copyright Kleinstein Lab, Yale University, 2018 Revision 9b7b6310370e.

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