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chewiesnake website  

ChewieSnake is an end-to-end cgMLST based workflow for analyzing a set of assemblies (or reads) and obtaining an easy-to-interpret cgMLST report.

  • ChewieSnake is a snakemake workflow that performs cgMLST allele calling for a set of assembled genomes using chewBBACA.
  • The workflow converts the resulting allele profiles into a nomenclature-free allele profile using allele hashes (following the idea of sistr).
  • The allele profiles of all input genomes are converted into an allele distance matrix, a minimum spanning tree and a neighbor-joining tree using grapetree.
  • The allele numbers in the nomenclature-free allele profiles are derived from the hashed allele sequences.

Therefore they can be directly compared between two or more laboratories without the need of an explicit exchange of the genome data, allele nomenclature or allele sequences.

  • If no assembly data is available, chewieSnake can assemble reads into draft genomes using fastp and shovill. See the --reads option.
  • Allele distances are hierarchically clustered and for each sample a cluster address as well as a unique (hashed) sequenced ID is provided.
  • The chewieSnake workflow returns highly-informative, interactive HTML reports.
  • The hashed allele profiles allow an inter-lab comparison with the chewieSnake_join workflow.

Environment Modules

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

System Variables

  • HPC_CHEWIESNAKE_DIR - installation directory
  • HPC_CHEWIESNAKE_EXE - executable directory


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

Deneke C, Uelze L, Brendebach H, Tausch SH and Malorny B (2021) Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST. Front. Microbiol. 12:649517. doi:10.3389/fmicb.2021.649517