changeo Logo
  • Immcantation Portal

Getting Started

  • Overview
  • Download
  • Installation
  • Contributing
  • Data Standards
  • Release Notes

Usage Documentation

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

Examples

  • Using IgBLAST
  • Parsing IMGT output
  • Parsing 10X Genomics V(D)J data
  • Filtering records
  • Clustering sequences into clonal groups
  • Reconstructing germline sequences
  • Generating MiAIRR compliant GenBank/TLS submissions

Methods

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

About

  • Contact
  • Citation
  • License
changeo
  • Commandline Usage
  • View page source

Commandline Usage

  • AlignRecords.py
    • AlignRecords.py across
    • AlignRecords.py block
    • AlignRecords.py within
  • AssignGenes.py
    • AssignGenes.py igblast
    • AssignGenes.py igblast-aa
  • BuildTrees.py
  • ConvertDb.py
    • ConvertDb.py airr
    • ConvertDb.py baseline
    • ConvertDb.py changeo
    • ConvertDb.py fasta
    • ConvertDb.py genbank
  • CreateGermlines.py
  • DefineClones.py
  • MakeDb.py
    • MakeDb.py igblast
    • MakeDb.py igblast-aa
    • MakeDb.py ihmm
    • MakeDb.py imgt
  • ParseDb.py
    • ParseDb.py add
    • ParseDb.py delete
    • ParseDb.py drop
    • ParseDb.py index
    • ParseDb.py merge
    • ParseDb.py rename
    • ParseDb.py select
    • ParseDb.py sort
    • ParseDb.py split
    • ParseDb.py update
Previous Next

© Copyright Kleinstein Lab, Yale University, 2025.

Built with Sphinx using a theme provided by Read the Docs.