PBcR

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1 Performance 2 0還沒 3 Dataset 6 (E.coli K-12 MG1655, 8 SMRT cells) 3.1 Performance 4 0.9 5 1.1 6 0.8 7 Dataset 7, (M. ruber DSM1279, 4 SMRT cells) 7.1 Performance 8 Dataset 8 (P. heparinus DSM1279, 7 SMRT cells) 8.1 Performance 9 Dataset 9 (E. coli K-12, P4-C2 chemistry, 20 Kbp, 1 SMRT cell) 9.1 Performance 9.2 wgs-8.2beta Performance

Performance

PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq
PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=4650000
PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=4185000
PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=5115000
PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=3720000
PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=5580000

0還沒

without genomeSize

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set	8 SMRT cells : 1st Set	8 SMRT cells : 2nd Set	8 SMRT cells : 3rd Set
# contigs	1	4	1	6	1	1	1	1	1	1
Largest contig	4 648 864	3 621 580	4 639 780	2 212 593	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
Total length	4 648 864	4 602 589	4 639 780	4 661 453	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
N50	4 648 864	3 621 580	4 639 780	887 256	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
Misassemblies
# misassemblies	10	8	8	8	8	8	10	9	8	8
Misassembled contigs length	4 648 864	3 621 580	4 639 780	3 857 726	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
Mismatches
# mismatches per 100kbp	0.19	0.54	0.37	0.34	0.17	0.09	0.15	0.34	0.09	0.11
# indels per 100kbp	1.59	24.54	22.42	15.82	6.38	10.22	5.63	4.38	5.32	6.06
# N's per 100kbp	0	0	0	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	100	99.169	99.965	99.981	100	100	100	100	100	100
Duplication ratio	1.002	1	1	1.003	1.003	1.001	1.002	1.002	1.002	1.002
# genes	4494+3 part	4458+8 part	4491+5 part	4491+6 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4493+3 part
NGA50	3 026 386	907 076	1 097 763	880 448	3 026 238	2 603 928	3 026 270	1 257 068	2 856 673	2 856 687
Running Time	12hr 14m	26m 16s	35m 50s	33m 3s	53m 36s	48m 9s	2hr 21m	2hr 43s	1hr 2m	53m 3s

genomeSize = 4650000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set	8 SMRT cells : 1st Set	8 SMRT cells : 2nd Set	8 SMRT cells : 3rd Set
# contigs	1	4	1	6	1	1	1	1	1	1
Largest contig	4 648 864	3 621 580	4 639 780	2 212 593	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
Total length	4 648 864	4 602 589	4 639 780	4 661 453	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
N50	4 648 864	3 621 580	4 639 780	887 256	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
Misassemblies
# misassemblies	10	8	8	8	8	8	10	9	8	8
Misassembled contigs length	4 648 864	3 621 580	4 639 780	3 857 726	4 651 575	4 645 728	4 647 827	4 649 239	4 648 687	4 648 099
Mismatches
# mismatches per 100kbp	0.19	0.54	0.37	0.34	0.17	0.09	0.15	0.34	0.09	0.11
# indels per 100kbp	1.59	24.54	22.42	15.82	6.38	10.22	5.63	4.38	5.32	6.06
# N's per 100kbp	0	0	0	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	100	99.169	99.965	99.981	100	100	100	100	100	100
Duplication ratio	1.002	1	1	1.003	1.003	1.001	1.002	1.002	1.002	1.002
# genes	4494+3 part	4458+8 part	4491+5 part	4491+6 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4493+3 part
NGA50	3 026 386	907 076	1 097 763	880 448	3 026 238	2 603 928	3 026 270	1 257 068	2 856 673	2 856 687
Running Time	12hr 14m	26m 16s	35m 50s	33m 3s	53m 36s	48m 9s	2hr 21m	2hr 43s	1hr 2m	53m 3s

genomeSize=4185000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set	8 SMRT cells : 1st Set	8 SMRT cells : 2nd Set	8 SMRT cells : 3rd Set
# contigs	2	6	1	6	1	1	1	1	1	1
Largest contig	4 644 985	3 621 592	4 639 809	2 212 597	4 651 574	4 645 691	4 647 833	4 649 261	4 648 735	4 648 123
Total length	4 656 267	4 640 061	4 639 809	4 650 332	4 651 574	4 645 691	4 647 833	4 649 261	4 648 735	4 648 123
N50	4 644 985	3 621 592	4 639 809	887 254	4 651 574	4 645 691	4 647 833	4 649 261	4 648 735	4 648 123
Misassemblies
# misassemblies	12	8	8	8	8	8	10	9	8	8
Misassembled contigs length	4 656 267	3 621 592	4 639 809	3 857 728	4 651 574	4 645 691	4 647 833	4 649 261	4 648 735	4 648 123
Mismatches
# mismatches per 100kbp	0.24	0.26	0.32	0.39	0.19	0.09	0.22	0.3	0.06	0.06
# indels per 100kbp	2.11	27.51	22.29	15.74	6.36	10.91	5.35	3.51	4.94	5.6
# N's per 100kbp	0	0	0	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	100	99.9	99.965	99.981	100	100	100	100	100	100
Duplication ratio	1.004	1.001	1	1.003	1.003	1.001	1.002	1.002	1.002	1.002
# genes	4494+3 part	4486+8 part	4491+5 part	4491+6 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part
NGA50	3 026 366	904 084	1 097 787	880 446	3 026 242	2 603 887	3 026 279	1 257 060	2 856 681	2 856 711
Running Time	10hr 1m	24m 51s	30m 28s	27m 44s	43m 13s	34m 39s	41m 29s	49m 7s	52m 10s	50m 29s

genomeSize=5115000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set	8 SMRT cells : 1st Set	8 SMRT cells : 2nd Set	8 SMRT cells : 3rd Set
# contigs	1	5	1	6	1	2	1	1	1	1
Largest contig	4 649 007	3 621 673	4 639 792	2 212 738	4 648 429	4 645 722	4 647 825	4 649 266	4 648 723	4 648 107
Total length	4 649 007	4 636 546	4 639 792	4 650 567	4 648 429	4 645 722	4 647 825	4 649 266	4 648 723	4 648 107
N50	4 649 007	3 621 673	4 639 792	887 256	4 648 429	4 645 722	4 647 825	4 649 266	4 648 723	4 648 107
Misassemblies
# misassemblies	10	8	8	8	8	8	10	9	8	8
Misassembled contigs length	4 649 007	3 621 673	4 639 792	3 857 870	4 648 429	4 645 722	4 647 825	4 649 266	4 648 723	4 648 107
Mismatches
# mismatches per 100kbp	0.17	0.32	0.41	0.37	0.19	0.11	0.15	0.39	0.06	0.11
# indels per 100kbp	1.53	25.72	22.34	15.84	6.21	10.32	5.63	3.53	5.17	6.06
# N's per 100kbp	0	0	0	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	100	99.9	99.965	99.981	100	100	100	100	100	100
Duplication ratio	1.002	1	1	1.003	1.002	1.001	1.002	1.002	1.002	1.002
# genes	4494 +3 part	4486 +8 part	4491 +5 part	4491 +6 part	4494 +3 part	4494 +3 part	4494 +3 part	4494 +3 part	4494 +3 part	4494 +3 part
NGA50	3 026 390	907 197	1 097 774	880 448	3 026 239	2 603 918	3 026 271	1 257 073	2 856 674	2 856 693
Running Time
Running Time	2hr 24m	26m 41s	33m 14s	30m 4s	47m 8s	37m 26s	46m 5s	54m 46s	59m 16s	56m 19s

genomeSize=3720000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set	8 SMRT cells : 1st Set	8 SMRT cells : 2nd Set	8 SMRT cells : 3rd Set
# contigs	1	6	1	6	1	1	1	1	1	1
Largest contig	4 648 264	3 621 566	4 639 815	2 212 780	4 651 567	4 654 368	4 647 818	4 649 190	4 648 720	4 648 103
Total length	4 648 264	4 640 025	4 639 815	4 649 418	4 651 567	4 654 368	4 647 818	4 649 190	4 648 720	4 648 103
N50	4 648 264	3 621 566	4 639 815	887 256	4 651 567	4 654 368	4 647 818	4 649 190	4 648 720	4 648 103
Misassemblies
# misassemblies	10	8	8	8	8	8	10	9	8	8
Misassembled contigs length	4 648 264	3 621 566	4 639 815	3 857 911	4 651 567	4 654 368	4 647 818	4 649 190	4 648 720	4 648 103
Mismatches
# mismatches per 100kbp	0.17	0.28	0.39	0.43	0.22	0.28	0.19	0.37	0.13	0.11
# indels per 100kbp	1.72	25.24	22.1	15.82	6.79	11.7	5.43	4.440	5.24	6.19
# N's per 100kbp	0	0	0	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	100	99.9	99.965	99.981	100	100	100	100	100	100
Duplication ratio	1.002	1.001	1	1.002	1.003	1.003	1.002	1.002	1.002	1.002
# genes	4494+3 part	4486+8 part	4491+5 part	4490+7 part	4494+3 part	4495+2 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part
NGA50	3 026 382	907 054	1 097 788	880 448	3 026 242	3 026 108	3 026 274	1 257 032	2 856 687	2 856 706
Running Time	1hr 45m	24m 2s	28m 45s	26m 23s	40m 12s	32m 31s	38m 38s	45m 55s	48m 40s	46m 47s

genomeSize=5580000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set	8 SMRT cells : 1st Set	8 SMRT cells : 2nd Set	8 SMRT cells : 3rd Set
# contigs	1	4	1	6	1	1	1	1	1	1
Largest contig	4 649 007	3 622 415	4 639 778	3 100 853	4 651 559	4 652 494	4 647 813	4 649 253	4 648 694	4 648 107
Total length	4 649 007	4 638 349	4 639 778	4 660 255	4 651 559	4 652 494	4 647 813	4 649 253	4 648 694	4 648 107
N50	4 649 007	3 622 415	4 639 778	3 100 853	4 651 559	4 652 494	4 647 813	4 649 253	4 648 694	4 648 107
Misassemblies
# misassemblies	10	8	8	8	8	9	10	9	8	8
Misassembled contigs length	4 649 007	3 622 415	4 639 778	3 858 736	4 651 559	4 652 494	4 647 813	4 649 253	4 648 694	4 648 107
Mismatches
# mismatches per 100kbp	0.19	0.43	0.37	0.34	0.15	0.09	0.15	0.37	0.11	0.11
# indels per 100kbp	1.51	25.84	22.42	15.88	6.4	10.35	5.73	3.66	5.22	6.06
# N's per 100kbp	0	0	0	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	100	99.937	99.965	100	100	100	100	100	100	100
Duplication ratio	1.002	1	1	1.004	1.003	1.003	1.002	1.002	1.002	1.002
# genes	4494+3 part	4488+8 part	4491+5 part	4492+5 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part	4494+3 part
NGA50	3 026 391	907 173	1 097 770	880 460	3 026 223	1 252 894	3 026 257	1 257 068	2 856 688	2 856 692
Running Time	2hr 9m	28m 59s	33m 32s	32m 21s	50m 17s	38m 36s	49m 13s	57m 6s	1hr 24s	59m 7s

Dataset 6 (E.coli K-12 MG1655, 8 SMRT cells)

We used all SMRT cells and randomly selected four and six SMRT cells three times for each, and evaluated the assemblies by QUAST against the reference genome (NC_000913) and Ec_gene_list. (more detail)

Performance

genomeSize=4650000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set
# contigs	2	51	44	76	6	6	6
Largest contig	3 835 938	300 354	500 180	250 542	2 045 145	2 044 223	2 542 485
Total length	4 640 874	4 437 792	4 476 210	4 297 112	4 636 889	4 635 531	4 645 642
N50	3 835 938	105 841	117 447	69 771	1 293 614	1 522 526	2 542 485
Misassemblies
# misassemblies	8	6	7	6	7	8	9
Misassembled contigs length	3 835 938	678 934	950 771	435 912	3 567 800	3 623 564	3 630 045
Mismatches
# mismatches per 100kbp	0.19	1.65	1.61	3.74	0.35	0.24	0.35
# indels per 100kbp	4.81	56.36	39.36	65.58	9.72	9.72	9.84
# N's per 100kbp	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	99.938	95.61	96.483	92.288	99.828	99.762	99.86
Duplication ratio	1.001	1.005	1.006	1.007	1.001	1.001	1.003
# genes	4490 +5 part	4229 +71 part	4288 +65 part	4094 +105 part	4481 +10 part	4475 +11 part	4485 +8 part
NGA50	949 276	89 654	111 935	53 222	857 569	857 671	859 217
Running Time	35m 5s	17m 43s	18m 14s	16m 12s	26m 17s	26m 9s	27m 2s

0.9

genomeSize=4185000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set
# contigs	2	50	45	75	7	6	7
Largest contig	3 835 933	300 354	500 170	250 539	2 044 974	2 044 226	2 177 146
Total length	4 640 868	4 437 828	4 476 213	4 279 289	4 636 194	4 635 257	4 641 795
N50	3 835 933	108 835	113 085	69 768	805 910	1 522 465	1 026 972
Misassemblies
# misassemblies	8	6	7	6	8	8	8
Misassembled contigs length	3 835 933	678 928	950 762	435 912	3 005 683	3 623 505	3 204 118
Mismatches
# mismatches per 100kbp	0.19	1.69	1.61	3.92	0.32	0.24	0.26
# indels per 100kbp	5.39	55.34	39.72	66.040	10.84	10.07	10.1
# N's per 100kbp	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	99.938	95.612	96.481	91.936	99.78	99.757	99.832
Duplication ratio	1.001	1	1	1.005	1.002	1.002	1.002
# genes	4490 +5 part	4230 +71 part	4287 +65 part	4081 +106 part	4476 +11 part	4475 +11 part	4484 +9 part
NGA50	949 260	91 700	98 453	53 221	805 910	857 615	770 513
Running Time	33m 51s	17m 26s	18m 7s	16m 23s	25m 54s	24m 48s	26m 8s

1.1

genomeSize = 5115000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set
# contigs	2	51	44	78	6	6	6
Largest contig	3 835 925	300 350	500 182	250 540	2 045 293	2 044 230	2 542 455
Total length	4 640 858	4 437 775	4 476 309	4 283 745	4 637 036	4 631 106	4 645 623
N50	3 835 925	105 842	117 459	60 082	1 293 612	1 522 478	2 542 455
Misassemblies
# misassemblies	8	6	7	6	7	7	9
Misassembled contigs length	3 835 925	678 925	950 766	435 899	356 7945	3 566 708	3 630 015
Mismatches
# mismatches per 100kbp	0.19	1.62	1.56	3.7	0.35	0.24	0.3
# indels per 100kbp	4.940	56.09	39.38	66.69	10.75	10.09	10.66
# N's per 100kbp	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	99.938	95.61	96.485	91.98	99.831	99.757	99.86
Duplication ratio	1.001	1	1	1.005	1.001	1.001	1.003
# genes	4490 +5 part	4229 +71 part	4288 +64 part	4085 +107 part	4481 +10 part	4474 +12 part	4485 +8 part
NGA50	949 271	89 653	111 937	53 221	857 567	857 628	859 219
Running Time	36m 41s	17m 52s	18m 22s	16m 44s	27m 49s	26m 54s	27m 59s

0.8

genomeSize=3720000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set
# contigs	2	51	45	74	10	7	7
Largest contig	3 835 918	300 357	499 793	250 543	1 068 976	2 044 231	2 177 132
Total length	4 640 911	4 429 199	4 462 499	4 252 687	4 637 980	4 633 643	4 641 751
N50	3 835 918	108 839	113 115	69 767	674 174	1 522 440	1 026 958
Misassemblies
# misassemblies	8	6	7	5	8	8	8
Misassembled contigs length	3 835 918	677 539	950 434	397 273	3 005 363	3 623 486	3 204 090
Mismatches
# mismatches per 100kbp	0.24	1.67	1.57	3.3	0.78	0.3	0.3
# indels per 100kbp	5.97	55.08	39.44	66	11.98	11.35	10.28
# N's per 100kbp	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	99.938	95.44	96.187	91.369	99.687	99.723	99.832
Duplication ratio	1.001	1	1	1.004	1.004	1.002	1.002
# genes	4490 +5 part	4221 +75 part	4274 +65 part	4056 +105 part	4467 +13 part	4471 +13 part	4484 +9 part
NGA50	949 257	91 700	98 451	53 254	618 553	857 595	770 508
Running Time	33m 1s	17m 3s	17m 19s	16m 9s	24m 53s	24m 12s	25m 13s

genomeSize=5580000

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set	6 SMRT cells : 1st Set	6 SMRT cells : 2nd Set	6 SMRT cells : 3rd Set
# contigs	4	52	44	76	6	6	3
Largest contig	3 161 528	300 351	500 181	250 537	2 045 299	2 044 231	3 622 857
Total length	4 662 182	4 441 307	4 483 671	4 298 734	4 637 078	4 631 147	4 635 596
N50	3 161 528	93 960	113 089	63 438	1 293 638	1 522 515	3 622 857
Misassemblies
# misassemblies	8	6	7	7	7 7	8
Misassembled contigs length	3 161 528	678 927	950 772	526 030	3 567 978	3 566 746	3 622 857
Mismatches
# mismatches per 100kbp	0.32	1.56	1.63	3.36	0.37	0.19	0.35
# indels per 100kbp	4.27	55.84	39.54	66.83	10.58	9.68	10.92
# N's per 100kbp	0	0	0	0	0	0	0
Genome Statistics
Genome fraction(%)	99.938	95.614	96.642	92.463	99.831	99.757	99.862
Duplication ratio	1.005	1.001	1	1.002	1.001	1.001	1.001
# genes	4490 +5 part	4230 +70 part	4293 +65 part	4105 +105 part	4481 +10 part	4474 +12 part	4487 +6 part
NGA50	702 757	89 630	111 935	53 224	857 595	857 662	910 332
Running Time	37m 36s	18m 7s	18m 27s	16m 51s	28m 57s	27m 36s	28m 25s

Dataset 7, (M. ruber DSM1279, 4 SMRT cells)

We used all SMRT cells to do assembly and evaluated the assemblies by QUAST against the reference genome (NC_013946) and Mr_gene_list. (more detail)

Performance

Statistics without reference	All Data
# contigs	2
Largest contig	2 974 307
Total length	3 100 289
N50	2 974 307
Misassemblies
# misassemblies	3
Misassembled contigs length	2 974 307
Mismatches
# mismatches per 100kbp	0.23
# indels per 100kbp	5.01
# N's per 100kbp	0.03
Genome Statistics
Genome fraction(%)	99.883
Duplication ratio	1.002
# genes	3093+4 part
NGA50	1 707 938
Running Time
pacBioToCA	7hr 35m
runCA	8hr 7m
Total	15hr 42m

Dataset 8 (P. heparinus DSM1279, 7 SMRT cells)

We used all SMRT cells and randomly selected four SMRT cells three times for each, and evaluated the assemblies by QUAST against the reference genome (NC_013061) and Ph_gene_list. (more detail)

Performance

Statistics without reference	All Data	4 SMRT cells : 1st Set	4 SMRT cells : 2nd Set	4 SMRT cells : 3rd Set
# contigs	1	3	3	3
Largest contig	5 163 983	2 232 679	2 236 613	2 237 949
Total length	5 163 983	5 161 276	5 165 518	5 166 563
N50	5 163 983	2 043 590	2 044 147	2 135 225
Misassemblies
# misassemblies	0	0	0	0
Misassembled contigs length	0	0	0	0
Mismatches
# mismatches per 100kbp	8.41	9.960	8.27	10.29
# indels per 100kbp	2.19	18.99	13.13	14.01
# N's per 100kbp	0	0	0	0
Genome Statistics
Genome fraction(%)	99.919	99.864	99.907	99.89
Duplication ratio	1	1	1.001	1.001
# genes	4335+3 part	4330+5 part	4333+5 part	4333+3 part
NGA50	5 163 983 532	2 043 590	2 044 147	2 135 225
Running Time
pacBioToCA	18hr 55m	6hr 27m	6hr 34m	6hr 31m
runCA	21hr 36m	11hr 39m	12hr 26m	12hr 12m
Total	40hr 31m	18hr 06m	19hr 00n	18hr 43m

Misassemblies for Adobe reader.

Dataset 9 (E. coli K-12, P4-C2 chemistry, 20 Kbp, 1 SMRT cell)

We used all SMRT cells and evaluated the assemblies by QUAST against the reference genome (NC_000913) and Ec_gene_list. (more detail)

Performance

Statistics without reference	All Data
# contigs	1
Largest contig	4 656257
Total length	4 656 257
N50	4 656 257
Misassemblies
# misassemblies	8
Misassembled contigs length	4 656 257
Mismatches
# mismatches per 100kbp	0.22
# indels per 100kbp	13.15
# N's per 100kbp	0
Genome Statistics
Genome fraction(%)	100
Duplication ratio	1.004
# genes	4494+3 part
NGA50	3 026 094
Running Time
PacBioToCA	13hr 01m
runCA	17hr 58m
Total	30hr 59m

We used the latest version of PBcR pipeline (8.2beta). more detail

PBcR -pbCNS -length 500 -partitions 200 -l p4c2 -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=4650000

wgs-8.2beta Performance

Statistics without reference	All Data
# contigs	2
Largest contig	4 644 060
Total length	4 652 830
N50	4 644 060
Misassemblies
# misassemblies	8
Misassembled contigs length	4 644 060
Mismatches
# mismatches per 100kbp	0.17
# indels per 100kbp	31.7
# N's per 100kbp	0
Genome Statistics
Genome fraction(%)	100
Duplication ratio	1.003
# genes	4494+3 part
NGA50	3 025 484
Running time
Running time	23m