. Author manuscript; available in PMC: 2013 Jul 10.

Published in final edited form as: Nat Biotechnol. 2012 Jul 1;30(7):693–700. doi: 10.1038/nbt.2280

Table 2. PacBio assembly contiguity.

Organism: The genome being assembled. The median and max lengths of corrected PacBio sequences (PBcR) are given in parenthesis. The corrected length is shorter than original PacBio RS sequences due to trimming and splitting chimeric sequences. Supplementary Table S2 reports the original PacBio RS sequence lengths before correction. The three reference data sets (Lambda NEB3011, E. coli K12, and S. cerevisiae S228c) were generated using the pre-release PacBio RS, resulting in shorter read lengths. Technology: the read data used for assembly. Pair separation (if applicable) is listed immediately after the coverage. Reference bp: the assumed genome size used for the N50 calculation. Assembly bp: the total number of base pairs in all contigs (only contigs ≥ 10,000 bp are included in all results). #Contigs: The number of contigs comprising the assembly. Max Contig Length: The maximum contig length. N50: N such that 50% of the genome is contained in contigs of length ≥ N. Assemblies for next-gen (Illumina/454) were generated by Celera Assembler,¹¹ SOAPdenovo,⁴⁹ and ALLPATHS-LG¹⁹ (where possible). Only the best assembly (based on contiguity) in each case was reported.

Organism	Technology	Reference bp	Assembly bp	# Contigs	Max Contig Length	N50
Lambda NEB3011	Illumina 100X 200bp	48 502	48 492	1	48 492 / 48 492	48 492 / 48 492 (100%) ^*
(median: 727 max: 3 280)	PacBio PBcR 25X		48 440	1	48 444 / 48 444	48 444 / 48 440 (100%) ^*

E. coli K12	Illumina 100X 500bp	4 639 675	4 462 836	61	221 615 / 221 553	100 338/ 83 037 (82.76%) ^*
(median: 747 max: 3 068 )	PacBio PBcR 18X		4 465 533	77	239 058 / 238 224	71 479/ 68 309 (95.57%) ^*
	PacBio PBcR 18X + Illumina 50X 500bp		4 576 046	65	238 272 / 238 224	93 048/ 89 431 (96.11%) ^*

S. cerevisiae S228c	Illumina 100X 300bp	12 157 105	11 034 156	192	266 528 / 227 714	73 871/ 49 254 (66.68%) ^*
(median: 674 max: 5 994)	PacBio PBcR 13X		11 110 420	224	224 478 / 217 704	62 898/ 54 633 (86.86%) ^*
	PacBio PBcR 13X + Illumina 50X 300bp		11 286 932	177	262 846 / 260 794	82 543/ 59 792 (72.44%) ^*

E. coli C227-11	PacBio CCS 50X	5 504 407	4 917 717	76	249 515	100 322
(median: 1 217 max: 14 901)	PacBio PBcR 25X (corrected by 25X CCS)		5 207 946	80	357 234	98 774
	PacBio PBcR 25X + CCS 25X		5 269 158	39	647 362	227 302
	PacBio PBcR 50X (corrected by 50X CCS)		5 445 466	35	1 076 027	376 443
	PacBio PBcR 50X + CCS 25X		5 453 458	33	1 167 060	527 198
	Manually Corrected ALLORA Assembly⁹		5 452 251	23	653 382	402 041

E. coli 17-2	Illumina 100X 300bp	5 000 000	4 975 331	62	226 141	74 940
(median: 886 max: 10 069 )	PacBio PBcR 50X		4 981 368	58	318 969	143 307
	PacBio PBcR 50X + Illumina 50X 300bp		5 022 503	55	367 911	180 932

E. coli JM221	454 50X	5 000 000	4 714 344	66	308 063	106 034
(median: 1 216 max: 12 552)	PacBio PBcR 25X		5 005 429	30	631 286	314 500
	PacBio PBcR 25X + 454 25X		5 008 824	30	633 667	314 500

Melopsittacus undulatus	Illumina 194X (220/500/800 paired-end 2/5/10Kb mate-pairs)	1.23 Gbp	1 023 532 850	24 181	1 050 202	47 383
	454 15.4X (FLX + FLX Plus + 3/8/20Kbp paired-ends)		999 168 029	16 574	751 729	75 178
(median: 1 182 max: 14 596)	454 15.4X + PacBio PBcR 3.83X (corrected by 15.4X 454)		1 066 348 480	15 328	871 294	93 069
(median: 997 max: 13 079)	454 15.4X + PacBio PBcR 3.75X (corrected by 54X Illumina)		1 071 356 415	15 081	1 238 843	99 573

For genomes with an available reference, the max and N50 contig is measured both before and after breaking contigs at assembly mis-joins. The percentages in parenthesis indicate the ratio between corrected and original N50. A higher ratio indicates a more correct assembly. Full assembly quality statistics are listed in Supplementary Table S4, following the GAGE assembly evaluation methodology.¹²