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''Staphylococcus aureus'' strain MW2. The ''S. aureu'' MW2 consists of a circular chromosome of 2.82 Mb and a plasmid of 20.7 kb in length, respectively.
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== Read source ==
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: The sequence reads were from the supplemental data ([http://genome.cshlp.org/content/18/5/802/suppl/DC1 supp data]) of David Hernandez et al.'s publication (Genome Research 2008). The data set is made up of 3.86 million of 35-bp reads.
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== Sequence assembly ==
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<table border=1>
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<tr><td>'''''Software'''''</td><td>'''''Version'''''</td><td>'''''Parameters'''''</td><td>'''''Download'''''</td></tr>
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<tr><td>ABySS</td><td>1.3.0</td><td>k=23</td><td>[[Media:S_Abyss_Contigs.fa|Abyss]]</td></tr>
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<tr><td>Velvet</td><td>1.1.04</td><td>k=23 min_contig_lgth=100 scaffolding=no</td><td>[[Media:S_Velvet_Contigs.fa|Velvet]]</td></tr>
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<tr><td>Edena</td><td>3</td><td>m=21</td><td>[[Media:S_Edena_Contigs.fa|Edena]]</td></tr>
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<tr><td>SOAPdenovo</td><td>1.05</td><td>K=23 M=3</td><td>[[Media:S_SOAPdenovo_Contigs.fa|SOAPdenovo]]</td></tr>
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</table>
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Merged File: [[Media:S_Contigs.fa|S_Contigs]]
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== Contig integrator ==
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<table border=1>
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<tr>
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<td>'''''Integrator'''''</td><td>'''''Download'''''</td>
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</tr>
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<tr><td>CISA</td><td>[[Media:CISA_S.fa|CISA]]</td></tr>
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<tr><td>minimus2</td><td>[[Media:minimus2_S.fa|minimus2]]</td></tr>
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</table>
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== Evaluation ==
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* '''Benchmark genome'''
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: [[Media:NC_003923_NC_005011.gbk|Staphylococcus aureus strain MW2]]
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* '''Evaluate by Mauve Assembly Metrics'''
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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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*'''Score with Mauve metrics:'''
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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;"|'''NumContigs'''
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| align="center" style="background:#f0f0f0;"|'''NumAssemblyBases'''
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| align="center" style="background:#f0f0f0;"|'''DCJ_Distance'''
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| align="center" style="background:#f0f0f0;"|'''NumMisCalled'''
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| align="center" style="background:#f0f0f0;"|'''NumUnCalled'''
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| align="center" style="background:#f0f0f0;"|'''NumGapsRef'''
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| align="center" style="background:#f0f0f0;"|'''NumGapsAssembly'''
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| align="center" style="background:#f0f0f0;"|'''TotalBasesMissed'''
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| align="center" style="background:#f0f0f0;"|'''%Missed'''
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| align="center" style="background:#f0f0f0;"|'''ExtraBases'''
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| align="center" style="background:#f0f0f0;"|'''%Extra'''
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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;"|'''ContigN50'''
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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:#eee685;"|'''Blast_IntactCDS'''
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|-
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| Velvet||1152||2775301||1124||49||0||1010||866||89319||3.1438||15087||0.5436||230||2421||5337||1329||22892||2265
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|-
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| ABySS||929||2769174||898||41||0||796||601||95493||3.3611||8641||0.312||171||2480||7793||1635||32717||2364
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|-
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| Edena||931||2757686||882||9||0||705||711||99275||3.4942||6966||0.2526||188||2463||6962||1672||37100||2331
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|-
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| SOAPdenovo||944||2781524||917||47||0||853||597||79607||2.802||11796||0.4241||166||2485||6386||1614||26967||2371
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|-bgcolor="#66CCFF"
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| CISA||665||2776133||635||48||0||571||388||79805||2.8089||5675||0.2044||100||2551||10533||2460||42008||2463
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|-
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| Minimus2(EVAS)||569||2769617||559||71||0||531||402||85573||3.012||7624||0.2753||107||2544||10672||2578||42022||2468
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