emmtyper

emmtyper

About : |

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

By default, we use the U.S. Centers for Disease Control and Prevention trimmed emm subtype database, which can be found here. The database is curated by Dr. Velusamy Srinivasan. We take this opportunity to thank Dr. Srinivasan for his work.

Documentation : https://github.com/MDU-PHL/emmtyper

Citation :

Directory tree :

emmtyper/
├── emmtyper_summary.tsv
└── sample_emmtyper.txt

Example file for an individual sample (sample_emmtyper.txt)

sample	Isolate name	Number of BLAST hits	Number of clusters	Predicted emm-type	Position(s)	Possible emm-like alleles	emm-like position(s)	EMM cluster
strep1_GCA_001412635.1	strep1_GCA_001412635.tmp	0	0	-	0:0	-	0:0	-

Example file for a run (emmtyper_summary.tsv)

sample	Isolate name	Number of BLAST hits	Number of clusters	Predicted emm-type	Position(s)	Possible emm-like alleles	emm-like position(s)	EMM cluster
strep1_GCA_001412635.1	strep1_GCA_001412635.tmp	0	0	-	0:0	-	0:0	-
strep1_GCA_016724885.1	strep1_GCA_016724885.tmp	0	0	-	0:0	-	0:0	-
strep1_GCA_900475035.1	strep1_GCA_900475035.tmp	7	3	EMM83.1	LS483338.1:1591916	EMM156.1~*;EMM240.1*	LS483338.1:1593307;LS483338.1:1590429	D4