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Welcome to VirMet

VirMet is a software suite designed to help users running viral metagenomics (mNGS) experiments: unspecific massively parallel NGS sequencing with the aim of discovering and characterizing the virus fraction of biological samples.

To see and download the code, visit our GitHub. Information on how to install VirMet can be found in the Installation section.

VirMet is called with a command-subcommand syntax. All the possible subcommands are:

  • fetch: download genomes
  • update: update viral database
  • index: index genomes
  • wolfpack: analyze a Miseq run or file
  • covplot: plot coverage for a specific organism

Some help can be obtained with virmet <subcommand> -h or simply virmet -h:

virmet -h
usage: virmet <command> [options]

positional arguments:
  {fetch,update,index,wolfpack,covplot}
                        available sub-commands
    fetch               download genomes
    update              update viral database
    index               index genomes
    wolfpack            analyze a Miseq run
    covplot             create coverage plot

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

Run `virmet subcommand -h` for more help

Enjoy using VirMet!