Version Differences for PBcR
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(→Performance)
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(→Performance)
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| ==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=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=4185000 | ||
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| 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=3720000 | ||
| PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=5580000 | PBcR -pbCNS -length 500 -partitions 200 -l ecoli -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=5580000 | ||
| + | without genomeSize | ||
| + | {| {{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 | 4]]||[[Media:pbcr_d5_rg4_2.fa | 1]]||[[Media:pbcr_d5_rg4_3.fa | 6]]||[[Media:pbcr_d5_rg6_1.fa | 1]]||[[Media:pbcr_d5_rg6_2.fa | 1]]||[[Media:pbcr_d5_rg6_3.fa | 1]]||[[Media:pbcr_d5_rg8_1.fa | 1]]||[[Media:pbcr_d5_rg8_2.fa | 1]]||[[Media:pbcr_d5_rg8_3.fa | 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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media: SCA_D5.pdf | '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''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 | ||
| + | |- | ||
| + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||12hr 14m||26m 16s||35m 50s||33m 3s||53m 36s||48m 9s||2hr 21m||2hr 43s||1hr 2m||53m 3s | ||
| + | |} | ||