Table 2.

Genome assembly statistics and comparison to reference genomes for insertions/deletions and rearrangements.

Organism	Assembly method	Library preparation method	Starting DNA quantity, ng	# of contigs	Total bps	Relative to the reference genomes
						Deletions	Insertions	Total indels	Rearrangements
B. anthracis	Allpaths	NEBNext	100	21	5,358,817	170	6,518	6,688	80
		TruSeq	1000	23	5,348,296	170	50,762	50,932	92
	IDBA	NEBNext	100	48	5,349,320	1,525	16,827	18,352	102
		TruSeq	1000	41	5,483,709	87,019	1,838	88,857	104
E. coli	Allpaths	NEBNext	100	82	5,312,046	758	48,753	49,511	222
		TruSeq	1000	96	5,269,849	760	80,227	80,987	238
	IDBA	NEBNext	100	199	5,216,101	111	152,190	152,301	414
		TruSeq	1000	207	5,242,710	224	75,926	76,150	446
B. thailandensis  A	Allpaths	NEBNext	10	26	6,652,405	100	12,213	12,313	80
		NEBNext	100	27	6,650,888	143	13,042	13,185	154
		TruSeq	1000	77	6,603,636	6,294	27,237	33,531	252
	IDBA	NEBNext	10	119	6,575,406	206	38,419	38,625	276
		NEBNext	100	117	6,575,500	351	38,382	38,733	280
		TruSeq	1000	271	6,582,658	8,320	35,337	43,657	586
B. thailandensis  B	Allpaths	NEBNext	10	23	6,660,010	144	12,576	12,720	82
		NEBNext	100	27	6,651,385	163	12,278	12,441	86
		TruSeq	1000	53	6,655,446	157	16,517	16,674	204
	IDBA	NEBNext	10	129	6,579,849	749	45,201	45,950	264
		NEBNext	100	125	6,579,749	236	44,279	44,515	262
		TruSeq	1000	281	6,587,931	8,694	45,997	54,691	612