Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

Table 3 Comparison of functions and features of different tools commonly used by the N. gonorrhoeae scientific community

	Gen2Epi	Sanger^α	Nullarbor	Pathogenwatch	pubMLST	NG-MAST	NG-STAR	SRST	NGMASTER	Patric
Data Cleaning	Yes	No	Yes	No	No	No	No	No	No	Yes
Contamination	Yes	No	Yes	No	No	No	No	No	No	Yes
Read Mapping	Yes	No	Yes	No	No	No	No	No	No	No
De novo assembly	Yes	No	Yes	No	No	No	No	No	No	Yes
Scaffolding	Yes	Yes	No	No	No	No	No	No	No	Yes
Plasmid assembly	Yes	No	No	No	No	No	No	No	No	Yes
Plasmid-type identification	Yes	No	No	No	No	No	No	No	No	No
Annotation	Yes	Yes	Yes	No	No	No	Yes	No	No	Yes
MAST	Yes	No	No	Yes	Yes	Yes	No	No	Yes	Yes
MLST	Yes	No	Yes	Yes	Yes	No	No	Yes	No	No
STAR	Yes	No	No	No	Yes	No	Yes	No	No	No
Tet Resistance	Yes	No	Yes	Yes	Yes	No	No	No	No	Yes
Usage	Command-line	Command-line	Command-line	Web-application	Web-application	Web-application	Web-application	Command-line	Command-line	Web-application
Output format	Text, FASTA	FASTA	Tabular, html	Tabular, html	Tabular, html	Tabular, html	Tabular, html	Text	Text	Tabular,html
Language	Perl	Perl	Perl	Unknown	Perl	Unknown	Perl	Python	Python	ECMAScript
Reference		20	29	21	6	12	10	8	13	47

ISSN: 1471-2164