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 The out-of-date files are removed and overwritten at the time of building and deployment.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
# 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>