Version Differences for PBcR
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(→Performance)
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(→Performance)
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| Line 320: | |||
| ==Performance== | ==Performance== | ||
| + | =1= | ||
| {| {{table}} border="1" | {| {{table}} border="1" | ||
| | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| Line 362: | |||
| |NGA50 ||859 464||621 281||572 455||436 292||1 098 529||1 096 784||859 502 | |NGA50 ||859 464||621 281||572 455||436 292||1 098 529||1 096 784||859 502 | ||
| |- | |- | ||
| - | | align="left" style="background:#f0f0f0;"|''' Running Time '''||2hr 9m||28m 59s||33m 32s||32m 21s||50m 17s||38m 36s||11m22c | + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||2hr 9m||28m 59s||33m 32s||32m 21s||50m 17s||38m 36s||11m22s |
| + | |} | ||
| + | =2= | ||
| + | {| {{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''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d6_all.fa | 2]]||[[Media:pbcr_d6_rg4_1.fa | 8]]||[[Media:pbcr_d6_rg4_2.fa | 10]]||[[Media:pbcr_d6_rg4_3.fa | 14]]||[[Media:pbcr_d6_rg6_1.fa | 1]]||[[Media:pbcr_d6_rg6_2.fa | 1]]||[[Media:pbcr_d6_rg6_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||2hr 9m||28m 59s||33m 32s||32m 21s||50m 17s||38m 36s||11m22s | ||
| + | |} | ||
| + | =3= | ||
| + | {| {{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''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d6_all.fa | 2]]||[[Media:pbcr_d6_rg4_1.fa | 8]]||[[Media:pbcr_d6_rg4_2.fa | 10]]||[[Media:pbcr_d6_rg4_3.fa | 14]]||[[Media:pbcr_d6_rg6_1.fa | 1]]||[[Media:pbcr_d6_rg6_2.fa | 1]]||[[Media:pbcr_d6_rg6_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||2hr 9m||28m 59s||33m 32s||32m 21s||50m 17s||38m 36s||11m22s | ||
| + | |} | ||
| + | =4= | ||
| + | {| {{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''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d6_all.fa | 2]]||[[Media:pbcr_d6_rg4_1.fa | 8]]||[[Media:pbcr_d6_rg4_2.fa | 10]]||[[Media:pbcr_d6_rg4_3.fa | 14]]||[[Media:pbcr_d6_rg6_1.fa | 1]]||[[Media:pbcr_d6_rg6_2.fa | 1]]||[[Media:pbcr_d6_rg6_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||2hr 9m||28m 59s||33m 32s||32m 21s||50m 17s||38m 36s||11m22s | ||
| + | |} | ||
| + | =5= | ||
| + | {| {{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''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d6_all.fa | 2]]||[[Media:pbcr_d6_rg4_1.fa | 8]]||[[Media:pbcr_d6_rg4_2.fa | 10]]||[[Media:pbcr_d6_rg4_3.fa | 14]]||[[Media:pbcr_d6_rg6_1.fa | 1]]||[[Media:pbcr_d6_rg6_2.fa | 1]]||[[Media:pbcr_d6_rg6_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||2hr 9m||28m 59s||33m 32s||32m 21s||50m 17s||38m 36s||11m22s | ||
| |} | |} | ||