Version Differences for Ecoli2

Line 1:
- abc   + ''Eshcherichia coli'' K12 MG1655  
       
    + == Read source ==  
       
    + : The illuminia read data of E coli (Paired-end sequencing library with 200 bp inserts) downloaded from Sequence Read Archive ([http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=SRR001665 SRA]).  
       
       
       
    + == Sequence assembly ==  
       
    + * '''Set1''' (Different Assemblers)  
       
    + <table border=1>  
    + <tr>  
    + <td>'''''Software'''''</td><td>'''''Version'''''</td><td>'''''Parameters'''''</td><td>'''''Download'''''</td>  
    + </tr>  
    + <tr><td>ABySS</td><td>1.3.0</td><td>k=31</td><td>[[Media:Abyss contigs.fa|Abyss]]</td></tr>  
    + <tr><td>Velvet</td><td>1.1.04</td><td>k=29 ins_length=215 cov_cutoff=12 exp_cov=24 min_contig_lgth=100 scaffolding=no</td><td>[[Media:Velvetcontigs.fa|Velvet]]</td></tr>  
    + <tr><td>Edena</td><td>3</td><td>m=30</td><td>[[Media:Edena contigs.fa|Edena]]</td></tr>  
    + <tr><td>SOAPdenovo</td><td>1.05</td><td>K=29 M=3</td><td>[[Media:SOAPdenovo contigs.fa|SOAPdenovo]]</td></tr>  
    + <tr><td>CLC</td><td>4.7.2</td><td>insert_size_range=194,236 minimum_contig_length=100</td><td>[[Media:CLC contigs.fa|CLC]]</td></tr>  
    + </table>  
    + Merged File: [[Media:Set1 Contigs.fa|Set1_Contig]]  
       
    + * '''Set2''' (Different parameters for Abyss - the assembler provides the lowest number of contigs in Set1)  
       
    + <table border=1>  
    + <tr>  
    + <td>'''''Abyss parameter'''''</td><td>'''''Download'''''</td>  
    + </tr>  
    + <tr><td>k=29</td><td>[[Media:Abyss contigs 29.fa|Abyss_k29]]</td></tr>  
    + <tr><td>k=31</td><td>[[Media:Abyss contigs 31.fa|Abyss_k31]]</td></tr>  
    + <tr><td>k=33</td><td>[[Media:Abyss contigs 33.fa|Abyss_k33]]</td></tr>  
    + </table>  
    + Merged File: [[Media:Set2 Contigs.fa|Set2_Contig]]  
       
    + * '''Set3''' (Different parameters for SOAPdenovo - the assembler provides the largest number of contigs in Set1)  
       
    + <table border=1>  
    + <tr>  
    + <td>'''''SOAPdenovo parameter'''''</td><td>'''''Download'''''</td>  
    + </tr>  
    + <tr><td>k=29</td><td>[[Media:Soap kmer29.fa|SOAP_k29]]</td></tr>  
    + <tr><td>k=31</td><td>[[Media:Soap kmer31.fa|SOAP_k31]]</td></tr>  
    + <tr><td>k=33</td><td>[[Media:Soap kmer33.fa|SOAP_k33]]</td></tr>  
    + </table>  
    + Merged File: [[Media:Set3 Contigs.fa|Set3_Contig]]  
       
       
    + == Contig integrator ==  
       
    + * '''CISA'''  
       
    + <table border=1>  
    + <tr>  
    + <td>'''''Input'''''</td><td>'''''Download'''''</td>  
    + </tr>  
    + <tr><td>[[Media:Set1 Contigs.fa|Set1]]</td><td>[[Media:CISA_Set1_Contigs.fa|CISA_Set1]]</td></tr>  
    + <tr><td>[[Media:Set2 Contigs.fa|Set2]]</td><td>[[Media:CISA_Set2_Contigs.fa|CISA_Set2]]</td></tr>  
    + <tr><td>[[Media:Set3 Contigs.fa|Set3]]</td><td>[[Media:CISA_Set3_Contigs.fa|CISA_Set3]]</td></tr>  
    + <tr><td>[[Media:Set_2_3_Contigs.fa|Set2+Set3]]</td><td>[[Media:CISA_Set2&3_Contigs.fa|CISA_Set2&3]]</td></tr>  
    + </table>  
       
    + * '''minimus2'''  
       
    + <table border=1>  
    + <tr>  
    + <td>'''''Input'''''</td><td>'''''Download'''''</td>  
    + </tr>  
    + <tr><td>Set1</td><td>[[Media:minimus2.fasta|minimus2_Set1]]</td></tr>  
    + </table>  
       
       
    + == Evaluation ==  
       
    + * '''Benchmark genome'''  
       
    + : [[Media:NC 000913.gbk|Eshcherichia coli K12 MG1655]]  
       
    + * '''Evaluate by Mauve Assembly Metrics'''  
       
    + : [http://code.google.com/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_Mauve How to score genome assemblies using the Mauve system]  
       
       
    + * '''Set1'''  
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Name'''  
    + | align="center" style="background:#f0f0f0;"|'''NumContigs'''  
    + | align="center" style="background:#f0f0f0;"|'''NumAssemblyBases'''  
    + | align="center" style="background:#f0f0f0;"|'''NumMisCalled'''  
    + | align="center" style="background:#f0f0f0;"|'''NumUnCalled'''  
    + | align="center" style="background:#f0f0f0;"|'''NumGapsRef'''  
    + | align="center" style="background:#f0f0f0;"|'''NumGapsAssembly'''  
    + | align="center" style="background:#f0f0f0;"|'''TotalBasesMissed'''  
    + | align="center" style="background:#f0f0f0;"|'''PercBasesMissed'''  
    + | align="center" style="background:#f0f0f0;"|'''ExtraBases'''  
    + | align="center" style="background:#f0f0f0;"|'''PercExtraBases'''  
    + | align="center" style="background:#f0f0f0;"|'''BrokenCDS'''  
    + | align="center" style="background:#f0f0f0;"|'''IntactCDS'''  
    + | align="center" style="background:#f0f0f0;"|'''ContigN50'''  
    + | align="center" style="background:#f0f0f0;"|'''ContigN90'''  
    + | align="center" style="background:#f0f0f0;"|'''MaxContigLength'''  
    + |-  
    + | Abyss||133||4626205||334||69||123||119||57847||1.2468||29424||0.636||57||4263||96157||26096||222425  
    + |-  
    + | CLC||379||4546926||100||0||288||287||130550||2.8138||3405||0.0749||62||4258||29767||8447||107342  
    + |-  
    + | Edena||211||4569446||17||0||129||125||86780||1.8704||2078||0.0455||66||4254||54405||13642||186686  
    + |-  
    + | SOAPdenovo||553||4547211||36||0||461||412||124407||2.6814||6972||0.1533||100||4220||17902||5384||103369  
    + |-  
    + | Velvet||283||4550675||138||0||208||203||116542||2.5119||2783||0.0612||74||4246||52474||12537||166094  
    + |-bgcolor="#66CCFF"  
    + | CISA_Set1||81||4625471||229||73||92||93||54849||1.1822||32166||0.6954||46||4274||113510||29195||268608  
    + |-  
    + | minimus2||74||4608653||285||0||97||78||76881||1.657||35464||0.7695||50||4270||126075||34542||417704  
    + |-  
    + |}  
       
    + * '''Set2-Set3'''  
    + {| {{table}} border="1"  
    + | align="center" style="background:#f0f0f0;"|'''Name'''  
    + | align="center" style="background:#f0f0f0;"|'''NumContigs'''  
    + | align="center" style="background:#f0f0f0;"|'''NumAssemblyBases'''  
    + | align="center" style="background:#f0f0f0;"|'''NumMisCalled'''  
    + | align="center" style="background:#f0f0f0;"|'''NumUnCalled'''  
    + | align="center" style="background:#f0f0f0;"|'''NumGapsRef'''  
    + | align="center" style="background:#f0f0f0;"|'''NumGapsAssembly'''  
    + | align="center" style="background:#f0f0f0;"|'''TotalBasesMissed'''  
    + | align="center" style="background:#f0f0f0;"|'''PercBasesMissed'''  
    + | align="center" style="background:#f0f0f0;"|'''ExtraBases'''  
    + | align="center" style="background:#f0f0f0;"|'''PercExtraBases'''  
    + | align="center" style="background:#f0f0f0;"|'''BrokenCDS'''  
    + | align="center" style="background:#f0f0f0;"|'''IntactCDS'''  
    + | align="center" style="background:#f0f0f0;"|'''ContigN50'''  
    + | align="center" style="background:#f0f0f0;"|'''ContigN90'''  
    + | align="center" style="background:#f0f0f0;"|'''MaxContigLength'''  
    + |-  
    + | Abyss_k29||130||4634010||322||30||118||115||61835||1.3327||40405||0.8719||54||4266||95691||26567||268182  
    + |-  
    + | Abyss_k31||133||4626205||334||69||123||119||57847||1.2468||29424||0.636||57||4263||96157||26096||222425  
    + |-  
    + | Abyss_k33||135||4644184||354||338||139||119||66355||1.4302||44937||0.9676||78||4242||89001||24907||268398  
    + |-bgcolor="#66CCFF"  
    + | CISA_Set2||105||4635199||332||130||117||103||55567||1.1976||39517||0.8525||63||4257||113377||27272||222663  
    + |-  
    + | SOAP_k29||1373||4582756||48||0||466||415||124372||2.6806||7247||0.1581||100||4220||17892||5276||103369  
    + |-  
    + | SOAP_k31||1295||4583165||56||0||510||466||121606||2.621||9201||0.2008||121||4199||17003||4286||77302  
    + |-  
    + | SOAP_k33||2170||4608265||105||0||1470||1380||126273||2.7216||41165||0.8933||507||3813||5391||1449||22953  
    + |-bgcolor="#66CCFF"  
    + | CISA_Set3||465||4546819||117||0||402||366||133247||2.8719||19266||0.4237||95||4225||21543||6065||103369  
    + |-bgcolor="#66CCHH"  
    + | CISA_Set2&3||105||4636783||351||160||118||104||54999||1.1854||39905||0.8606||60||4260||113377||27272||222663  
    + |-  
    + |}