Main tool : emmtyper
'emmtyper' is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly.
- Andre Tan
- Torsten Seemann
- Jake Lacey
- Mark Davies
- Liam Mcintyre
- Hannah Frost
- Deborah Williamson
- Anders Gonçalves da Silva
The codebase for emmtyper was primarly written by Andre Tan as part of his Master's
Degree in Bioinformatics. Torsten Seemann, Deborah Williamson, and Anders Gonçalves da Silva provided supervision and assistance.
Hannah Frost contributed with EMM clustering by suggesting we incorporate it in to the code, and providing the necessary information to do so and test it.
Jake Lacey, Liam Mcintyre, and Mark Davies provided assistance in validating emmtyper.
The code is actively maintained by MDU Bioinformatics Team.
Contact the principal maintainer at andersgs at gmail dot com.
# 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>