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Kourami is a tool for assembling HLA haplotypes. It uses high coverage whole genome sequencing data and implements a graph-guided assembly method for classical HLA genes, which is capable of discovering new HLA alleles.


Sequence assembly


  • Operation: Sequence assembly; localised reassembly
  • Input: BAM
  • Output: FASTA
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; MAC OS X
  • License: BSD-3-Clause
  • Cost: Free
  • Version name: 0.9.6
  • Credit: Gordon and Betty Moore Foundation;National Science Foundation;U.S. National Institutes of Health;The Shurl and Kay Curci Foundation
  • Contact: carlk _at_
  • Collection: -


Lee H, Kingsford C "Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery." Genome Biol. 2018 Feb 7;19(1):16.
PMID: 29415772
PMCID: PMC5804087

Download and documentation

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