Version Differences for PBcR

(→Performance)
Line 16:
  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   + without genomeSize([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D5/wogSize/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 65:
  |}    |} 
       
- genomeSize = 4650000   + genomeSize = 4650000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D5/gSize/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 114:
  |}    |} 
       
- genomeSize=4185000   + genomeSize=4185000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D5/gSize-10/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 163:
  |}    |} 
       
- genomeSize=5115000   + genomeSize=5115000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D5/gSize+10/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 214:
  |}    |} 
       
- genomeSize=3720000   + genomeSize=3720000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D5/gSize-20/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 264:
       
       
- genomeSize=5580000   + genomeSize=5580000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D5/gSize+20/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 325:
       
  ==Performance==    ==Performance== 
- genomeSize=4650000   + genomeSize=4650000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D6/gSize/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 372:
  |}    |} 
       
- genomeSize=4185000   + genomeSize=4185000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D6/gSize-10/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 418:
  |}    |} 
       
- genomeSize = 5115000   + genomeSize = 5115000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D6/gSize+10/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 464:
  |}    |} 
       
- genomeSize=3720000   + genomeSize=3720000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D6/gSize-20/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 510:
  |}    |} 
       
- genomeSize=5580000   + genomeSize=5580000 ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D6/gSize+20/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 611:
  ==Performance==    ==Performance== 
       
- without genomeSize   + without genomeSize ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D7/wogSize/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 657:
       
       
- with genomeSize   + with genomeSize ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D7/wgSize/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 700:
  | align="left" style="background:#f0f0f0;"|''' Running Time '''||34m 23s||34m 5s||41m||34m 12s||43m 56s    | align="left" style="background:#f0f0f0;"|''' Running Time '''||34m 23s||34m 5s||41m||34m 12s||43m 56s 
  |}    |} 
       
       
  =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]) 
- ==Performance==      
       
  PBcR -pbCNS -length 500 -partitions 200 -l phep -s pacbio.spec -fastq filtered_subreads.fastq    PBcR -pbCNS -length 500 -partitions 200 -l phep -s pacbio.spec -fastq filtered_subreads.fastq 
Line 711:
  PBcR -pbCNS -length 500 -partitions 200 -l phep -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=6204000    PBcR -pbCNS -length 500 -partitions 200 -l phep -s pacbio.spec -fastq filtered_subreads.fastq genomeSize=6204000 
       
- without genomeSize   + ==Performance==  
    + without genomeSize ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/wogSize/report.html more detail])  
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 753:
  | align="left" style="background:#f0f0f0;"|''' Running Time '''||1hr 11m||53m 55s||54m 57s||57m 8s    | align="left" style="background:#f0f0f0;"|''' Running Time '''||1hr 11m||53m 55s||54m 57s||57m 8s 
  |}    |} 
- genomeSize= 5170000 bp      
       
    + genomeSize= 5170000 bp ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/gSize/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
  | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''    | align="center" style="background:#f0f0f0;"|'''Statistics without reference ''' 
Line 797:
  |}    |} 
       
- genomeSize= 4653000 bp   + genomeSize= 4653000 bp ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/gSize-10/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 841:
  |}    |} 
       
- genomeSize= 5687000 bp   + genomeSize= 5687000 bp ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/gSize+10/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 886:
       
       
- genomeSize = 4136000 bp   + genomeSize = 4136000 bp ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/gSize-20/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 930:
  |}    |} 
       
- genomeSize= 6204000 bp   + genomeSize= 6204000 bp ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/gSize+20/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 976:
       
       
- without genomeSize and pbCNS   + without genomeSize and pbCNS ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D8/nopbcns_wogSize/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 1031:
  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 
       
- with different genomeSize   + with different genomeSize ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D9/wgSize/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1" 
Line 1077:
       
       
- without genomeSize   + without genomeSize ([http://sb.nhri.org.tw/comps/quast/Non-hybrid/wgs-8.2/D9/wogSize/report.html more detail])  
       
  {| {{table}} border="1"    {| {{table}} border="1"