Version Differences for PBcR

(→Dataset 8 (P. heparinus DSM1279, 7 SMRT cells))
(→1)
Line 740:
  |}    |} 
  [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader.    [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader. 
       
    + =1=  
       
    + {| {{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'''  
    + |-  
    + |# contigs||[[Media: pbcr_d8_all.fa | 1]]||[[Media: pbcr_d8_rg4_1.fa | 3]]||[[Media: pbcr_d8_rg4_2.fa | 3]]||[[Media: pbcr_d8_rg4_3.fa | 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  
    + |-  
    + | style="background:#f0f0f0;"| [[Media:sca_d8.pdf | '''Misassemblies''']]||||||||  
    + |-  
    + |# misassemblies||0||0||0||0  
    + |-  
    + |Misassembled contigs length ||0||0||0||0  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |}  
    + [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader.  
       
    + =1=  
       
    + {| {{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'''  
    + |-  
    + |# contigs||[[Media: pbcr_d8_all.fa | 1]]||[[Media: pbcr_d8_rg4_1.fa | 3]]||[[Media: pbcr_d8_rg4_2.fa | 3]]||[[Media: pbcr_d8_rg4_3.fa | 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  
    + |-  
    + | style="background:#f0f0f0;"| [[Media:sca_d8.pdf | '''Misassemblies''']]||||||||  
    + |-  
    + |# misassemblies||0||0||0||0  
    + |-  
    + |Misassembled contigs length ||0||0||0||0  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |}  
    + [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader.  
       
    + =1=  
       
    + {| {{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'''  
    + |-  
    + |# contigs||[[Media: pbcr_d8_all.fa | 1]]||[[Media: pbcr_d8_rg4_1.fa | 3]]||[[Media: pbcr_d8_rg4_2.fa | 3]]||[[Media: pbcr_d8_rg4_3.fa | 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  
    + |-  
    + | style="background:#f0f0f0;"| [[Media:sca_d8.pdf | '''Misassemblies''']]||||||||  
    + |-  
    + |# misassemblies||0||0||0||0  
    + |-  
    + |Misassembled contigs length ||0||0||0||0  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |}  
    + [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader.  
       
    + =1=  
       
    + {| {{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'''  
    + |-  
    + |# contigs||[[Media: pbcr_d8_all.fa | 1]]||[[Media: pbcr_d8_rg4_1.fa | 3]]||[[Media: pbcr_d8_rg4_2.fa | 3]]||[[Media: pbcr_d8_rg4_3.fa | 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  
    + |-  
    + | style="background:#f0f0f0;"| [[Media:sca_d8.pdf | '''Misassemblies''']]||||||||  
    + |-  
    + |# misassemblies||0||0||0||0  
    + |-  
    + |Misassembled contigs length ||0||0||0||0  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |}  
    + [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader.  
       
    + =1=  
       
    + {| {{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'''  
    + |-  
    + |# contigs||[[Media: pbcr_d8_all.fa | 1]]||[[Media: pbcr_d8_rg4_1.fa | 3]]||[[Media: pbcr_d8_rg4_2.fa | 3]]||[[Media: pbcr_d8_rg4_3.fa | 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  
    + |-  
    + | style="background:#f0f0f0;"| [[Media:sca_d8.pdf | '''Misassemblies''']]||||||||  
    + |-  
    + |# misassemblies||0||0||0||0  
    + |-  
    + |Misassembled contigs length ||0||0||0||0  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |-  
    + | style="background:#f0f0f0;"| '''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  
    + |}  
    + [[Media: sca_d8_summary.pdf | '''Misassemblies''']] for Adobe reader.  
  =Dataset 9 (''E. coli'' K-12, P4-C2 chemistry, 20 Kbp, 1 SMRT cell)=    =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 ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/PBcR_pipeline/D9/report.html more detail])    We used all SMRT cells and evaluated the assemblies by QUAST against the reference genome ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/ NC_000913]) and [[Media: Ec_gene_result.ncbi | Ec_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/PBcR_pipeline/D9/report.html more detail])