Table 1.

Summary of sequencing projects used in the pipeline development

Strain ID	Sequence typea	Serogroupb	Geographic originc	Date collected	Genome size	Closest referenced	Substitutions per position versus ref.e	Total reads	Total bases sequenced	Average read length	Coveragef	Instrument standardg
Neisseria meningitidis
NM13220	ST-7	A	Philippines	2005	2.2M	Z2491	0.076	197 067	47 569 493	241	21×	GS-20
NM10699	ST-32	B	Oregon, USA	2003	2.2M	MC58	0.053	418 751	81 775 264	195	37×	GS-20
NM15141	ST-11	C	New York, USA	2006	2.2M	FAM18	0.028	378 773	94 288 660	249	42×	GS-20
NM9261	ST-11	W135	Burkina Faso	2002	2.2M	FAM18	0.030	206 634	69 957 473	338	31×	GS Ti
NM18575	ST-2859	A	Burkina Faso	2003	2.2M	Z2491	0.033	283 888	84 013 571	296	38×	GS Ti
NM5178	ST-32	B	Oregon, USA	1998	2.2M	MC58	0.050	270 332	88 664 981	328	40×	GS Ti
NM15293	ST-32	B	Georgia, USA	2006	2.2M	MC58	0.054	276 733	90 951 566	329	41×	GS Ti
Bordetella bronchiseptica
BBE001	N/Ah	N/A	Georgia, USA	1956	5.3M	RB50	0.056	566 834	229 098 141	404	43×	GS Ti
BBF579	N/A	N/A	Mississippi, USA	2007	5.3M	RB50	0.104	533 099	228 467 710	429	43×	GS Ti

Data for each strain are presented in rows.

^aSequence type denotes the allelic profile assigned by multilocus sequence typing (MLST; Holmes et al., 1999; Maiden et al., 1998) on the basis of seven loci within well-conserved house-keeping genes.

^bNeisseria meningitidis isolates are divided into serogroups by immunochemistry of polysaccharides present in their antiphagocytic capsule.

^cThe region in which each strain was originally collected.

^dStrain ID of the closest complete genome available in GenBank, as determined by 16S RNA phylogeny as well as whole-genome sequence identity, which agreed in all cases.

^eInsertions, deletions and substitutions per position of genome as compared against the closest reference.

^fCoverage denotes the average number of sequencing reads overlapping at a given position in the genome, calculated as the total number of bases sequenced divided by the estimated length of the genome.

^gThe standard of the 454 pyrosequencing instrument and reagents used to sequence the data.

^hSequence typing and serotyping was not performed on B.bronchiseptica.