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Mercury is a tool for validating genomes assembled using long read sequencing. The algorithm uses k-mer to evaluate base accuracy and completeness of a genome by comparing the de novo assembled genome with high accuracy reads that are not used in the assembly. The program does not require another reference assembly for its evaluation. It is able to evaluate the haplotype-specific accuracy, completeness, phase block continuity and switch errors in trio binned assemblies.


Sequence assembly


  • Operation: Genome assembly assessment
  • Software interface: Command-line user interface
  • Language: R, Java, sh
  • Operating system: Linux; Mac OS
  • License: Not stated
  • Cost: Free
  • Version name: 1.1
  • Credit: Members of the Vertebrate Genomes Project assembly.
  • Contact: arang.rhie _at_
  • Collection: -


Rhie A, Walenz BP, Koren S, Phillippy AM "Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies." Genome Biol, 2020
PMID: 32928274
PMCID: PMC7488777

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