Version Differences for PBcR
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(→Performance)
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(→Performance)
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| Line 67: | |||
| |} | |} | ||
| + | {| {{table}} border="1" | ||
| + | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''All Data''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d5_all.fa | 1]]||[[Media:pbcr_d5_rg4_1.fa | 1]]||[[Media:pbcr_d5_rg4_2.fa | 1]]||[[Media:pbcr_d5_rg4_3.fa | 5]]||[[Media:pbcr_d5_rg6_1.fa | 2]]||[[Media:pbcr_d5_rg6_2.fa | 2]]||[[Media:pbcr_d5_rg6_3.fa | 1]]||[[Media:pbcr_d5_rg8_1.fa | 4]]||[[Media:pbcr_d5_rg8_2.fa | 1]]||[[Media:pbcr_d5_rg8_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media: SCA_D5.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |} | ||
| + | {| {{table}} border="1" | ||
| + | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''All Data''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d5_all.fa | 1]]||[[Media:pbcr_d5_rg4_1.fa | 1]]||[[Media:pbcr_d5_rg4_2.fa | 1]]||[[Media:pbcr_d5_rg4_3.fa | 5]]||[[Media:pbcr_d5_rg6_1.fa | 2]]||[[Media:pbcr_d5_rg6_2.fa | 2]]||[[Media:pbcr_d5_rg6_3.fa | 1]]||[[Media:pbcr_d5_rg8_1.fa | 4]]||[[Media:pbcr_d5_rg8_2.fa | 1]]||[[Media:pbcr_d5_rg8_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media: SCA_D5.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |} | ||
| + | {| {{table}} border="1" | ||
| + | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''All Data''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d5_all.fa | 1]]||[[Media:pbcr_d5_rg4_1.fa | 1]]||[[Media:pbcr_d5_rg4_2.fa | 1]]||[[Media:pbcr_d5_rg4_3.fa | 5]]||[[Media:pbcr_d5_rg6_1.fa | 2]]||[[Media:pbcr_d5_rg6_2.fa | 2]]||[[Media:pbcr_d5_rg6_3.fa | 1]]||[[Media:pbcr_d5_rg8_1.fa | 4]]||[[Media:pbcr_d5_rg8_2.fa | 1]]||[[Media:pbcr_d5_rg8_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media: SCA_D5.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |} | ||
| + | {| {{table}} border="1" | ||
| + | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''All Data''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d5_all.fa | 1]]||[[Media:pbcr_d5_rg4_1.fa | 1]]||[[Media:pbcr_d5_rg4_2.fa | 1]]||[[Media:pbcr_d5_rg4_3.fa | 5]]||[[Media:pbcr_d5_rg6_1.fa | 2]]||[[Media:pbcr_d5_rg6_2.fa | 2]]||[[Media:pbcr_d5_rg6_3.fa | 1]]||[[Media:pbcr_d5_rg8_1.fa | 4]]||[[Media:pbcr_d5_rg8_2.fa | 1]]||[[Media:pbcr_d5_rg8_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media: SCA_D5.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |} | ||