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''Escherichia coli'' K12 MG1655. The ''E. coli'' MG1655 consists of a circular chromosome of 4,639,675 bp in length.
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== Read source ==
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: The paired-end illuminia read data of ''E. coli'' were downloaded from Illumina ([ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/Ecoli_MG1655_PE_bfast.bam |Illumina]) with a median insert size of 214 bp. More than 28.4 M 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=75</td><td>[[Media:E100_Abyss_Contigs.fa|Abyss]]</td></tr>
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<tr><td>Velvet</td><td>1.1.04</td><td>VelvetOptimiser --s 59 --e 97</td><td>[[Media:E100_Velvet_Contigs.fa|Velvet]]</td></tr>
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<tr><td>Edena</td><td>3</td><td>m=75</td><td>[[Media:E100_Edena_Contigs.fa|Edena]]</td></tr>
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<tr><td>SOAPdenovo</td><td>1.05</td><td>k=75 M=3 avg_ins=215</td><td>[[Media:E100_SOAPdenovo_Contigs.fa|SOAPdenovo]]</td></tr>
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</table>
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Merged File: [[Media:E100_Contigs.fa|E100_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_E100.fa|CISA]]</td></tr>
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<tr><td>minimus2</td><td>[[Media:minimus2_E100_1.fa|minimus2(AEVS)]],[[Media:minimus2_E100_2.fa|minimus2(ASEV)]], [[Media:minimus2_E100_3.fa|minimus2(ASVE)]], [[Media:minimus2_E100_4.fa|minimus2(ESAV)]],[[Media:minimus2_E100_5.fa|minimus2(ESVA)]], [[Media:minimus2_E100_6.fa|minimus2(SEAV)]], [[Media:minimus2_E100_7.fa|minimus2(SEVA)]], [[Media:minimus2_E100_8.fa|minimus2(SVAE)]], [[Media:minimus2_E100_9.fa|minimus2(VASE)]], [[Media:minimus2_E100_10.fa|minimus2(VEAS)]]</td></tr>
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<tr><td>GAA</td><td>[[Media:GAA_E100_1.fa|GAA(AESV)]],[[Media:GAA_E100_2.fa|GAA(AEVS)]], [[Media:GAA_E100_3.fa|GAA(ASEV)]], [[Media:GAA_E100_4.fa|GAA(EASV)]],[[Media:GAA_E100_5.fa|GAA(EAVS)]], [[Media:GAA_E100_6.fa|GAA(ESAV)]], [[Media:GAA_E100_7.fa|GAA(EVAS)]], [[Media:GAA_E100_8.fa|GAA(EVSA)]], [[Media:GAA_E100_9.fa|GAA(VAES)]], [[Media:GAA_E100_10.fa|GAA(VASE)]]</td></tr>
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</table>
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Beacuase minimus2 and GAA merge two assemblies at a time, we iteratively integrate the four assemblies in random order.
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== Evaluation ==
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* '''Benchmark genome'''
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: [[Media:NC 000913.gbk|Eshcherichia coli K12 MG1655]]
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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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| 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;"|'''cor.Units'''
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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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|-
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| Abyss||190||4642915||119||125||75||147||128||50280||1.0837||23618||0.5087||76||4244||66424||20680||222412||4243||135||68544||134||68545||3,(0,0,3)
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| Edena||421||4584984||331||22||0||281||271||86700||1.8687||6753||0.1473||145||4175||24375||6689||104739||4048||377||24375||373||24375||3,(1,1,1)
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|-
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| SOAPdenovo||560||4596003||272||100||0||245||256||112014||2.4143||6408||0.1394||111||4209||31788||7901||105615||4105||356||31837||358||31837||3,(1,0,2)
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| Velvet||264||4569720||191||127||33||204||210||102966||2.2193||3936||0.0861||92||4228||46975||11116||161713||4159||228||46975||241||44024||16,(4,7,5)
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|-bgcolor="#66CCFF"
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| CISA||110||4641820||106||156||64||153||120||44382||0.9566||39138||0.8432||69||4251||77896||25720||222524||4248||106||79212||118||70571||12,(3,4,5)
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| minimus2||94 ||4588207 ||88 ||233 ||0 ||129 ||103 ||322633 ||6.9538||209679 ||4.5169||76 ||4244 ||86379 ||27964 ||225809 ||4077 ||94 ||88183 ||107 ||68430 ||13,(6,3,4)
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| GAA||311 ||4636486 ||222 ||105 ||39 ||216 ||197 ||59416 ||1.2806||22776 ||0.4906||107 ||4213 ||48108 ||13772 ||162326 ||4152 ||261 ||50871 ||248 ||47458 ||6,(3,1,2)
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Please note that the scores of minimus2 and GAA were taken from the average of ten random combinations.
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