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smudgeplot website  

This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.

Environment Modules

Run module spider smudgeplot to find out what environment modules are available for this application.

System Variables

  • HPC_SMUDGEPLOT_DIR - installation directory
  • HPC_SMUDGEPLOT_BIN - executable directory


If you publish research that uses smudgeplot you have to cite it as follows:

Ranallo-Benavidez, T.R., Jaron, K.S. & Schatz, M.C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11, 1432 (2020).