Version Differences for PBcR
|
(→wgs-8.2beta Performance)
|
(→Performance)
|
| Line 555: | |||
| | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' | ||
| | align="center" style="background:#f0f0f0;"|'''All Data''' | | 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_d7_all.fa | 2]] | + | |# contigs||[[Media:pbcr_d6_all.fa | 2]]||[[Media:pbcr_d6_rg4_1.fa | 51]]||[[Media:pbcr_d6_rg4_2.fa | 44]]||[[Media:pbcr_d6_rg4_3.fa | 76]]||[[Media:pbcr_d6_rg6_1.fa | 6]]||[[Media:pbcr_d6_rg6_2.fa | 6]]||[[Media:pbcr_d6_rg6_3.fa | 6]] |
| + | |- | ||
| + | |Largest contig||3 835 938||300 354||500 180||250 542||2 045 145||2 044 223||2 542 485 | ||
| |- | |- | ||
| - | |Largest contig||2 974 307 | + | |Total length||4 640 874||4 437 792||4 476 210||4 297 112||4 636 889||4 635 531||4 645 642 |
| |- | |- | ||
| - | |Total length||3 100 289 | + | |N50||3 835 938||105 841||117 447||69 771||1 293 614||1 522 526||2 542 485 |
| |- | |- | ||
| - | |N50||2 974 307 | + | | style="background:#f0f0f0;"| [[Media:SCA_d6.pdf | '''Misassemblies''']]|||||||||||||| |
| |- | |- | ||
| - | | style="background:#f0f0f0;"| [[Media:sca_d7.pdf | '''Misassemblies''']]|| | + | |# misassemblies||8||6||7||6||7||8||9 |
| |- | |- | ||
| - | |# misassemblies||3 | + | |Misassembled contigs length ||3 835 938||678 934||950 771||435 912||3 567 800||3 623 564||3 630 045 |
| |- | |- | ||
| - | |Misassembled contigs length ||2 974 307 | + | | style="background:#f0f0f0;"| '''Mismatches'''|||||||||||||| |
| |- | |- | ||
| - | | style="background:#f0f0f0;"| '''Mismatches'''|| | + | |# mismatches per 100kbp||0.19||1.65||1.61||3.74||0.35||0.24||0.35 |
| |- | |- | ||
| - | |# mismatches per 100kbp||0.23 | + | |# indels per 100kbp||4.81||56.36||39.36||65.58||9.72||9.72||9.84 |
| |- | |- | ||
| - | |# indels per 100kbp||5.01 | + | |# N's per 100kbp ||0||0||0||0||0||0||0 |
| |- | |- | ||
| - | |# N's per 100kbp ||0.03 | + | | style="background:#f0f0f0;"| '''Genome Statistics'''|||||||||||||| |
| |- | |- | ||
| - | | style="background:#f0f0f0;"| '''Genome Statistics'''|| | + | |Genome fraction(%) ||99.938||95.61||96.483||92.288||99.828||99.762||99.86 |
| |- | |- | ||
| - | |Genome fraction(%) ||99.883 | + | |Duplication ratio ||1.001||1.005||1.006||1.007||1.001||1.001||1.003 |
| |- | |- | ||
| - | |Duplication ratio ||1.002 | + | |# genes ||4490 +5 part||4229 +71 part||4288 +65 part||4094 +105 part||4481 +10 part||4475 +11 part||4485 +8 part |
| |- | |- | ||
| - | |# genes ||3093+4 part | + | |NGA50 ||949 276||89 654||111 935||53 222||857 569||857 671||859 217 |
| |- | |- | ||
| - | |NGA50 ||1 707 938 | + | | align="left" style="background:#f0f0f0;"|''' Running Time '''||35m 5s||17m 43s||18m 14s||16m 12s||26m 17s||26m 9s||27m 2s |
| - | |- | ||
| - | | style="background:#f0f0f0;"| '''Running Time'''|| | ||
| - | |- | ||
| - | |pacBioToCA||7hr 35m | ||
| - | |- | ||
| - | |runCA||8hr 7m | ||
| - | |- | ||
| - | |Total||15hr 42m | ||
| |} | |} | ||
| =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]) | ||