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Kermit is a tool for using linkage maps to guide genome assembly. It simplifies assembly and reduce assembly errors for users with long-read based data for contig assembly. Linkage maps are often used to validate the assembly but, in this tool, these maps are used to guide the assembly instead of being used post-contig assembly. It implements a coloured overlap graphs strategy.


Sequence assembly


  • Operation: Sequence assembly; De novo assembly; linkage maps
  • Software interface: command-line user interface
  • Language: C
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: Academy of Finland; Jane and Aatos Erkko Foundation
  • Contact: -
  • Collection: -


Walve R, Rastas P, Salmela L "Kermit: linkage map guided long read assembly." Algorithms Mol Biol. 2019 Mar 20;14:8. eCollection 2019.
PMID: 30930956
PMCID: PMC6425630

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