Table 2:

Metrics of the S288C assemblies after polishing. Assemblies were corrected using 300x of 2 × 250 bp Illumina reads as input to Pilon. The resulting corrected assembly was then aligned to the S288C reference genome using Quast.

	Spades	Canu	Miniasm	SMARTdenovo	ABruijn
Reads dataset used	Illumina PE 2 × 250 bp	2D pass	Canu-corrected	Longest 2D	2D
Coverage	300x	67x	108x	30x	120x
# reads > 10 kb	0	16 860	21 005	28 668	28 668
# contigs	376	37	28	26	23
Cumulative size	12 047 788	12 230 747	12 113 521	12 213 590	12 182 847
Genome fraction (%)	96.464	98.519	98.421	99.352	98.635
N50	149 184	610 494	736 456	783 336	816 355
N90	19 522	191 846	265 917	242 658	257 117
L50	27	8	7	7	6
L90	100	20	16	16	16
# mismatches	1126	1898	4455	4205	2138
# mismatches per 100 kb	9.47	15.85	37.23	34.27	17.88
# insertions	81	1657	3164	2384	1325
# deletions	439	1869	5208	5551	1838
# deletions in homopolymers	38	868	4248	4023	740
# indels per 100 kb	1.97	22.49	57.27	46.76	21.76
# genes	6087 + 177 partial	6241 + 32 partial	6215 + 37 partial	6266 + 33 partial	6243 + 45 partial
# genes without indels	6023	5921	5475	5881	6002