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
1
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 |
0.37 |
2.49 |
1.88 |
5.38 |
0.69 |
0.67 |
0.86 |
| # indels per 100kbp |
3.58 |
53.34 |
45.82 |
73.07 |
10.65 |
11.28 |
10.46 |
| # N's per 100kbp |
0 |
0.04 |
0.02 |
0.09 |
0 |
0 |
0 |
| Genome Statistics |
|
|
|
|
|
|
|
| Genome fraction(%) |
99.993 |
99.733 |
99.67 |
99.693 |
99.972 |
99.946 |
99.968 |
| Duplication ratio |
1.002 |
1.005 |
1.006 |
1.007 |
1.001 |
1.001 |
1.003 |
| # genes |
4492+5 part |
4475+10 part |
4467+12 part |
4469+13 part |
4492+4 part |
4491+4 part |
4492+4 part |
| NGA50 |
859 464 |
621 281 |
572 455 |
436 292 |
1 098 529 |
1 096 784 |
859 502 |
| Running Time |
2hr 9m |
28m 59s |
33m 32s |
32m 21s |
50m 17s |
38m 36s |
11m22s |
4
| 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 |
8 |
10 |
14 |
1 |
1 |
4 |
| Largest contig |
4 278 957 |
2 277 010 |
1 213 670 |
984 459 |
4 641 350 |
4 640 250 |
3 162 440 |
| Total length |
4 650 771 |
4 648 304 |
4 644 602 |
4 656 274 |
4 641 350 |
4 640 250 |
4 653 394 |
| N50 |
4 278 957 |
622 425 |
800 993 |
565 251 |
4 641 350 |
4 640 250 |
3 162 440 |
| Misassemblies |
|
|
|
|
|
|
|
| # misassemblies |
9 |
9 |
9 |
8 |
8 |
8 |
9 |
| Misassembled contigs length |
4 278 957 |
2 809 129 |
2 085 482 |
1 947 163 |
4 641 350 |
4 640 250 |
3 209 090 |
| Mismatches |
|
|
|
|
|
|
|
| # mismatches per 100kbp |
0.37 |
2.49 |
1.88 |
5.38 |
0.69 |
0.67 |
0.86 |
| # indels per 100kbp |
3.58 |
53.34 |
45.82 |
73.07 |
10.65 |
11.28 |
10.46 |
| # N's per 100kbp |
0 |
0.04 |
0.02 |
0.09 |
0 |
0 |
0 |
| Genome Statistics |
|
|
|
|
|
|
|
| Genome fraction(%) |
99.993 |
99.733 |
99.67 |
99.693 |
99.972 |
99.946 |
99.968 |
| Duplication ratio |
1.002 |
1.005 |
1.006 |
1.007 |
1.001 |
1.001 |
1.003 |
| # genes |
4492+5 part |
4475+10 part |
4467+12 part |
4469+13 part |
4492+4 part |
4491+4 part |
4492+4 part |
| NGA50 |
859 464 |
621 281 |
572 455 |
436 292 |
1 098 529 |
1 096 784 |
859 502 |
| Running Time |
2hr 9m |
28m 59s |
33m 32s |
32m 21s |
50m 17s |
38m 36s |
11m22s |
5
| 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 |
8 |
10 |
14 |
1 |
1 |
4 |
| Largest contig |
4 278 957 |
2 277 010 |
1 213 670 |
984 459 |
4 641 350 |
4 640 250 |
3 162 440 |
| Total length |
4 650 771 |
4 648 304 |
4 644 602 |
4 656 274 |
4 641 350 |
4 640 250 |
4 653 394 |
| N50 |
4 278 957 |
622 425 |
800 993 |
565 251 |
4 641 350 |
4 640 250 |
3 162 440 |
| Misassemblies |
|
|
|
|
|
|
|
| # misassemblies |
9 |
9 |
9 |
8 |
8 |
8 |
9 |
| Misassembled contigs length |
4 278 957 |
2 809 129 |
2 085 482 |
1 947 163 |
4 641 350 |
4 640 250 |
3 209 090 |
| Mismatches |
|
|
|
|
|
|
|
| # mismatches per 100kbp |
0.37 |
2.49 |
1.88 |
5.38 |
0.69 |
0.67 |
0.86 |
| # indels per 100kbp |
3.58 |
53.34 |
45.82 |
73.07 |
10.65 |
11.28 |
10.46 |
| # N's per 100kbp |
0 |
0.04 |
0.02 |
0.09 |
0 |
0 |
0 |
| Genome Statistics |
|
|
|
|
|
|
|
| Genome fraction(%) |
99.993 |
99.733 |
99.67 |
99.693 |
99.972 |
99.946 |
99.968 |
| Duplication ratio |
1.002 |
1.005 |
1.006 |
1.007 |
1.001 |
1.001 |
1.003 |
| # genes |
4492+5 part |
4475+10 part |
4467+12 part |
4469+13 part |
4492+4 part |
4491+4 part |
4492+4 part |
| NGA50 |
859 464 |
621 281 |
572 455 |
436 292 |
1 098 529 |
1 096 784 |
859 502 |
| Running Time |
2hr 9m |
28m 59s |
33m 32s |
32m 21s |
50m 17s |
38m 36s |
11m22s |
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 |
