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emmtyper container

Main tool : emmtyper

Code repository: https://github.com/MDU-PHL/emmtyper

Basic information on how to use this tool:

  • executable: emmtyper
  • help: --help
  • version: --version
  • description: |

'emmtyper' is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly.

Additional information:

This image uses the most up-to-date fasta file for emm typing by downloading from https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa. The out-of-date files are removed and overwritten at the time of building and deployment.

Full documentation: https://github.com/MDU-PHL/emmtyper

Example Usage

# run emmtyper in BLAST (default) mode:

emmtyper <file name(s)>.fasta -o <output_file>

# or with output written in verbose format:

emmtyper <file name(s)>.fasta -o <output_file> -f verbose

# run emmtyper in PCR mode (useful for troubleshooting, see documentation)

emmtyper -w pcr <file name(s)>.fasta -o <output_file_2>