Version Differences for PBcR
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(→Performance)
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(→Performance)
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| | align="left" style="background:#f0f0f0;"|''' Running Time '''||35m 5s||17m 43s||18m 14s||16m 12s||26m 17s | | align="left" style="background:#f0f0f0;"|''' Running Time '''||35m 5s||17m 43s||18m 14s||16m 12s||26m 17s | ||
| |} | |} | ||
| + | =123= | ||
| + | {| {{table}} border="1" | ||
| + | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''All Data''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''3 SMRT cells : 1st Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''3 SMRT cells : 2nd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''3 SMRT cells : 3rd Set''' | ||
| + | | align="center" style="background:#f0f0f0;"|'''3 SMRT cells : 4th Set''' | ||
| + | |- | ||
| + | |# contigs||[[Media:pbcr_d6_all.fa | 1]]||[[Media:pbcr_d6_rg4_1.fa | 1]]||[[Media:pbcr_d6_rg4_2.fa | 1]]||[[Media:pbcr_d6_rg4_3.fa | 1]]||[[Media:pbcr_d6_rg6_1.fa | 1]] | ||
| + | |- | ||
| + | |Largest contig||3 100 062||3 099 663||3 099 663||3 098 784||3 099 602 | ||
| + | |- | ||
| + | |Total length||3 100 062||3 099 663||3 099 663||3 098 784||3 099 602 | ||
| + | |- | ||
| + | |N50||3 100 062||3 099 663||3 099 663||3 098 784||3 099 602 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''Misassemblies''']]|||||||||| | ||
| + | |- | ||
| + | |# misassemblies||0||0||0||0||0 | ||
| + | |- | ||
| + | |Misassembled contigs length ||0||0||0||0||0 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''Mismatches'''|||||||||| | ||
| + | |- | ||
| + | |# mismatches per 100kbp||0.03||0.06||0.06||0.03||0.03 | ||
| + | |- | ||
| + | |# indels per 100kbp||13.53||20.47||20.47||19.95||20.7 | ||
| + | |- | ||
| + | |# N's per 100kbp ||0||0||0||0||0 | ||
| + | |- | ||
| + | | style="background:#f0f0f0;"| '''Genome Statistics'''|||||||||| | ||
| + | |- | ||
| + | |Genome fraction(%) ||99.986||99.986||99.986||99.986||99.986 | ||
| + | |- | ||
| + | |Duplication ratio ||1.001||1.001||1.001||1.001||1.001 | ||
| + | |- | ||
| + | |# genes ||3103 + 2part||3103 +2 part||3103 +2 part||3103 +2 part||3103 +2 part | ||
| + | |- | ||
| + | |NGA50 ||3 100 062||3 099 663||3 099 663||3 098 784||3 099 602 | ||
| + | |- | ||
| + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||35m 5s||17m 43s||18m 14s||16m 12s||26m 17s | ||
| + | |} | ||
| =Dataset 8 (''P. heparinus'' DSM1279, 7 SMRT cells)= | =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 ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Pedobacter_heparinus_DSM_2366_uid59111/ NC_013061]) and [[Media:gene_phep.ncbi | Ph_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/PBcR_pipeline/D8/report.html more detail]) | 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 ([ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Pedobacter_heparinus_DSM_2366_uid59111/ NC_013061]) and [[Media:gene_phep.ncbi | Ph_gene_list]]. ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/PBcR_pipeline/D8/report.html more detail]) | ||