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mash container

Main tool: mash

Code repository: https://github.com/marbl/Mash

Additional tools:

  • none

Basic information on how to use this tool:

  • executable: mash
  • help: -h
  • version: --version
  • description: Fast genome and metagenome distance estimation using MinHash

Additional information:

This container includes a custom reference sketch at /db/cbird-v2.0-lite.msh
The sketch contains only the species of Acinetobacter, Burkholderia, Citrobacter, Enterobacter, Escherichia, Klebsiella, Kluyvera, Metapseudomonas, Morganella, Neisseria, Proteus, Providencia, Pseudomonas, Raoultella, Salmonella, Serratia, Streptococcus
The full list of sketched genomes are here.

Full documentation: https://mash.readthedocs.io/en/latest/

Example Usage

# genome vs. genome
mash dist genome1.fna genome2.fna
# multiple genomes vs. genome
mash dist reference.msh genome.fna
# screen against refseq
mash screen refseq.genomes.msh genome.fq > screen.tab