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Getting Started

  • Overview
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  • Installation
  • 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
  • IgPhyML lineage tree analysis
  • Generating MiAIRR compliant GenBank/TLS submissions

Methods

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

About

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Commandline UsageΒΆ

  • 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
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© Copyright Kleinstein Lab, Yale University, 2022. Revision 2cc7614f.

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