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: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Staphylococcus_aureus_USA300_TCH1516_uid58925/ S. aureus USA300_TCH1516] |
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: [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Staphylococcus_aureus_USA300_TCH1516_uid58925/ S. aureus USA300_TCH1516] |
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* '''Evaluated by Mauve Assembly Metrics to calculate the values for the left columns of "Blast_IntactCDS"'''
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* '''Evaluated by Mauve Assembly Metrics to calculate the values for the left columns of "N50, Blast_IntactCDS"'''
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: [http://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve How to score genome assemblies using the Mauve system]
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: [http://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve How to score genome assemblies using the Mauve system] (mauve_linux_snapshot_2011-08-31)
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* '''Evaluated by Blast with Features''' |
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* '''Evaluated by Blast with Features''' |
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: [http://gage.cbcb.umd.edu/index.html Gage] |
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: [http://gage.cbcb.umd.edu/index.html Gage] |
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*'''Score with Mauve metrics:'''
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*'''Score with Mauve Assembly Metrics, N50, Blast and GAGE:'''
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{| {{table}} border="1" |
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{| {{table}} border="1" |
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| align="center" style="background:#f0f0f0;"|'''Name''' |
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| align="center" style="background:#f0f0f0;"|'''Name''' |
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| align="center" style="background:#f0f0f0;"|'''BrokenCDS''' |
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| align="center" style="background:#f0f0f0;"|'''BrokenCDS''' |
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| align="center" style="background:#f0f0f0;"|'''IntactCDS''' |
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| align="center" style="background:#f0f0f0;"|'''IntactCDS''' |
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| align="center" style="background:#f0f0f0;"|'''ContigN50'''
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| align="center" style="background:#f0f0f0;"|'''ContigN50^'''
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| align="center" style="background:#f0f0f0;"|'''ContigN90''' |
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| align="center" style="background:#f0f0f0;"|'''ContigN90''' |
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| align="center" style="background:#f0f0f0;"|'''MaxContigLength''' |
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| align="center" style="background:#f0f0f0;"|'''MaxContigLength''' |
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| align="center" style="background:#f0f0f0;"|'''!N50'''
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| align="center" style="background:#eee685;"|'''N50^'''
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| align="center" style="background:#eee685;"|'''Blast_IntactCDS''' |
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| align="center" style="background:#eee685;"|'''Blast_IntactCDS''' |
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| align="center" style="background:#f0f0f0;"|'''Units(>200)''' |
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| align="center" style="background:#f0f0f0;"|'''Units(>200)''' |
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| align="center" style="background:#f0f0f0;"|'''N50'''
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| align="center" style="background:#f0f0f0;"|'''N50^'''
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| align="center" style="background:#f0f0f0;"|'''cor.Units''' |
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| align="center" style="background:#f0f0f0;"|'''cor.Units''' |
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| align="center" style="background:#f0f0f0;"|'''cor.N50'''
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| align="center" style="background:#f0f0f0;"|'''cor.N50^'''
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| align="center" style="background:#f0f0f0;"|'''Errors,(Indel>=5,Inv,Rel)''' |
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| align="center" style="background:#f0f0f0;"|'''Errors,(Indel>=5,Inv,Rel)''' |
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[^] Please note that the ContigN50 calculated by Mauve Assembly Metrics is incorrect (off-by-one error). We have followed the definition of N50 (''A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.'' [http://www.ncbi.nlm.nih.gov/pubmed/22510764 ref]) to calculate N50s. GAGE's N50 was calculated using the total reference genome length rather than the sum total of contig lengths. The GAGE's cor.N50 values were computed after correcting contigs by breaking them at each error.
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[#] Please note that GAA and minimus2 were designed to merge two assemblies at a time, we thus performed [http://sb.nhri.org.tw/CISA/en/Saureus_101_all2 all runs] and took the average scores. |
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[#] Please note that GAA and minimus2 were designed to merge two assemblies at a time, we thus performed [http://sb.nhri.org.tw/CISA/en/Saureus_101_all2 all runs] and took the average scores. |
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