PBcR

Revision as of 12 December 2014 01:17 by admin (Comments | Contribs) | (→0.9)



Contents

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

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

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 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

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 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

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 8 SMRT cells : 1st Set 8 SMRT cells : 2nd Set 8 SMRT cells : 3rd Set
# contigs 1 1 1 5 2 2 1 4 1 2
Largest contig 4 651 604 4 647 117 4 648 057 3 447 068 3 749 516 2 770 859 4 649 699 1 679 082 4 649 323 4 189 785
Total length 4 651 604 4 647 117 4 648 057 4 661 453 4 645 941 4 657 272 4 649 699 4 655 949 4 649 323 4 652 482
N50 4 651 604 4 647 117 4 648 057 3 447 068 3 749 516 2 770 859 4 649 699 1 159 845 4 649 323 4 189 785
Misassemblies
# misassemblies 9 9 8 9 7 9 10 7 10 8
Misassembled contigs length 4 651 604 4 647 117 4 648 057 3 447 068 4 645 941 4 657 272 4 649 699 2 143 406 4 649 323 4 189 785
Mismatches
# mismatches per 100kbp 0.34 1.03 0.69 0.78 0.69 0.56 0.58 0.75 0.84 0.75
# indels per 100kbp 0.6 7.44 5.78 5.67 1.88 2.72 1.66 1.6 1.9 2.65
# N's per 100kbp 0 0.02 0 0 0 0 0 0 0.02 0
Genome Statistics
Genome fraction(%) 100 100 100 99.949 99.956 100 100 99.959 100 99.993
Duplication ratio 1.003 1.002 1.002 1.005 1.002 1.005 1.002 1.004 1.002 1.003
# genes 4494+3 part 4494+3 part 4494+3 part 4490+5 part 4491+2 part 4495+2 part 4494+3 part 4489+6 part 4494+3 part 4493+4 part
NGA50 2 834 925 949 217 949 242 656 513 2 796 469 1 040 965 3 026 388 949 298 3 027 267 949 289
Running Time
PacBioToCA 48hr 16m 4hr 58m 5hr 48m 5hr 10m 11hr 09m 9hr 34m 10hr 47m 21hr 06m 22hr 05m 21hr 23m
runCA 15hr 48m 15hr 22m 13hr 50m 11hr 20m 12hr 38m 11hr 44m 13hr 48m 11hr 37m 14hr 36m 13hr 40m
Total 64hr 04m 20hr 20m 19hr 38m 16hr 30m 23hr 47m 21hr 18m 24hr 35m 32hr 43m 36hr 41m 25hr 03m

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 8 SMRT cells : 1st Set 8 SMRT cells : 2nd Set 8 SMRT cells : 3rd Set
# contigs 1 1 1 5 2 2 1 4 1 2
Largest contig 4 651 604 4 647 117 4 648 057 3 447 068 3 749 516 2 770 859 4 649 699 1 679 082 4 649 323 4 189 785
Total length 4 651 604 4 647 117 4 648 057 4 661 453 4 645 941 4 657 272 4 649 699 4 655 949 4 649 323 4 652 482
N50 4 651 604 4 647 117 4 648 057 3 447 068 3 749 516 2 770 859 4 649 699 1 159 845 4 649 323 4 189 785
Misassemblies
# misassemblies 9 9 8 9 7 9 10 7 10 8
Misassembled contigs length 4 651 604 4 647 117 4 648 057 3 447 068 4 645 941 4 657 272 4 649 699 2 143 406 4 649 323 4 189 785
Mismatches
# mismatches per 100kbp 0.34 1.03 0.69 0.78 0.69 0.56 0.58 0.75 0.84 0.75
# indels per 100kbp 0.6 7.44 5.78 5.67 1.88 2.72 1.66 1.6 1.9 2.65
# N's per 100kbp 0 0.02 0 0 0 0 0 0 0.02 0
Genome Statistics
Genome fraction(%) 100 100 100 99.949 99.956 100 100 99.959 100 99.993
Duplication ratio 1.003 1.002 1.002 1.005 1.002 1.005 1.002 1.004 1.002 1.003
# genes 4494+3 part 4494+3 part 4494+3 part 4490+5 part 4491+2 part 4495+2 part 4494+3 part 4489+6 part 4494+3 part 4493+4 part
NGA50 2 834 925 949 217 949 242 656 513 2 796 469 1 040 965 3 026 388 949 298 3 027 267 949 289
Running Time
PacBioToCA 48hr 16m 4hr 58m 5hr 48m 5hr 10m 11hr 09m 9hr 34m 10hr 47m 21hr 06m 22hr 05m 21hr 23m
runCA 15hr 48m 15hr 22m 13hr 50m 11hr 20m 12hr 38m 11hr 44m 13hr 48m 11hr 37m 14hr 36m 13hr 40m
Total 64hr 04m 20hr 20m 19hr 38m 16hr 30m 23hr 47m 21hr 18m 24hr 35m 32hr 43m 36hr 41m 25hr 03m

1.2

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 1 1 5 2 2 1 4 1 2
Largest contig 4 651 604 4 647 117 4 648 057 3 447 068 3 749 516 2 770 859 4 649 699 1 679 082 4 649 323 4 189 785
Total length 4 651 604 4 647 117 4 648 057 4 661 453 4 645 941 4 657 272 4 649 699 4 655 949 4 649 323 4 652 482
N50 4 651 604 4 647 117 4 648 057 3 447 068 3 749 516 2 770 859 4 649 699 1 159 845 4 649 323 4 189 785
Misassemblies
# misassemblies 9 9 8 9 7 9 10 7 10 8
Misassembled contigs length 4 651 604 4 647 117 4 648 057 3 447 068 4 645 941 4 657 272 4 649 699 2 143 406 4 649 323 4 189 785
Mismatches
# mismatches per 100kbp 0.34 1.03 0.69 0.78 0.69 0.56 0.58 0.75 0.84 0.75
# indels per 100kbp 0.6 7.44 5.78 5.67 1.88 2.72 1.66 1.6 1.9 2.65
# N's per 100kbp 0 0.02 0 0 0 0 0 0 0.02 0
Genome Statistics
Genome fraction(%) 100 100 100 99.949 99.956 100 100 99.959 100 99.993
Duplication ratio 1.003 1.002 1.002 1.005 1.002 1.005 1.002 1.004 1.002 1.003
# genes 4494+3 part 4494+3 part 4494+3 part 4490+5 part 4491+2 part 4495+2 part 4494+3 part 4489+6 part 4494+3 part 4493+4 part
NGA50 2 834 925 949 217 949 242 656 513 2 796 469 1 040 965 3 026 388 949 298 3 027 267 949 289
Running Time
PacBioToCA 48hr 16m 4hr 58m 5hr 48m 5hr 10m 11hr 09m 9hr 34m 10hr 47m 21hr 06m 22hr 05m 21hr 23m
runCA 15hr 48m 15hr 22m 13hr 50m 11hr 20m 12hr 38m 11hr 44m 13hr 48m 11hr 37m 14hr 36m 13hr 40m
Total 64hr 04m 20hr 20m 19hr 38m 16hr 30m 23hr 47m 21hr 18m 24hr 35m 32hr 43m 36hr 41m 25hr 03m


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

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
pacBioToCA 20hr 03m 5hr 52m 6hr 05m 5hr 19m 15hr 53m 14hr 47m 15hr 38m
runCA 15hr 41m 7hr 32m 7hr 10m 5hr 42m 15hr 44m 16hr 02m 13hr 27m
Total 35hr 44m 13hr 24m 13hr 15m 11hr 01m 31hr 37m 30hr 49m 29hr 05m

Misassemblies for Adobe reader.

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