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= Prerequisites =
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* Linux 64-bit environment
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[http://www.centos.org CentOS]
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* Python 2.X
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[http://www.python.org Python]<br>
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- Under centos: yum install python
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* MUMmer 3.22 or higher
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[http://mummer.sourceforge.net MUMmer]
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* Blast 2.2.25+ or higher
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[http://blast.ncbi.nlm.nih.gov Blast+]
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= Installation =
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Please unpack the tar file.<br>
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[[Media:CISA_20120425.tar|CISA - 2012.04.25]]
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Available commands:
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>tar xvf CISA.tar
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Execute access:
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>chmod 755 -R CICA1.0
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== Commands and configuration ==
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=== Merge.py ===
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Mergy.py can convert data format to fit CISA. '''This is an essentail pre-work'''.
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Available commands:
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>python Merge.py Merge.config
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The content of configuration file:
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count=3
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data=assembly1.fasta,title=Contig_m1
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data=assembly2.fasta,title=Contig_m2
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data=assembly3.fasta,title=Contig_m3
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Master_file=Contigs_m.fa
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min_length=100 (default:100)
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Gap=11
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#count<br>The number of assemblies you would like to merge
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#min_length<br>Contigs of length smaller than min_length (e.g. 100 bp) will be discarded.
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#Gap<br>It's an optional variable.<br>With this variable, we will split the assemblies into contigs at >10 Ns.
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Please note that '''dos2unix''' may be necessary if your data are in DOS/MAC format.
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>dos2unix assembly1.fasta assembly2.fasta assembly3.fasta
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=== CISA.py ===
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Available commands:
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>python CISA.py CISA.config
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The content of configuration file:
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genome=genome size
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infile=file
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outfile=file
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nucmer=your installed path/nucmer
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R2_Gap=0.95 (default:0.95)
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CISA=your installed path/CISA1.0
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makeblastdb=your installed path/makeblastdb
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blastn=your installed path/blastn
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#genome<br/>Please input the estimated genome size here. The longest length of your input assemblies will be recommended. <br/>The break point of CISA will be set to 1.1 * genome variable.
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#infile<br/>The file containing the set of contigs you want to integrate.
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#nucmer<br/>The executive file for nucmer. If nucmer has been added into the path, this variable can be skipped.
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#makeblastdb<br/>The executive file for makeblastdb. If makeblastdb has been added into the path, this variable can be skipped.
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#blastn<br/>The executive file for blastn. If blastn has been added into the path, this variable can be skipped.
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#CISA<br/>Home directory of CISA.
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#R2_Gap<br/>A threshold used in the phase 2 of CISA.
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== Example ==
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<ul><li><strong>Prepair datasets:</strong> At least three assemblies are required for contig integration using CISA.</li></ul>
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<blockquote>In the case of [[Ecoli|Ecoli]], we used five softwares including Abyss, CLC, Edena, SOAPdenovo and Velvet to generate five assemblies.</blockquote>
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<ul><li><strong>Convert the format and ID of your datasets:</strong><br/></li></ul>
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<blockquote><p> The content of the configuration file (Merge.config):</p></blockquote>
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<table width="457" border="1">
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<tr>
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<td height="152" align="left" bgcolor="#66CCFF">
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count=5
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data=Abyss_contigs.fa,title=Abyss
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data=Edena_contigs.fa,title=Edena
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data=SOAPdenovo_contigs.fa,title=SOAP
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data=CLC_contigs.fa,title=CLC
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data=Velvet_contigs.fa,title=Velvet
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Master_file=Contigs.fa
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</td>
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</tr>
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</table>
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<ul><li><strong>Command:</strong><br /></li></ul><blockquote><p>>python Merge.py Merge.config</p></blockquote>
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Input files: [[Media:Abyss contigs.fa|Abyss_contigs.fa]], [[Media:Edena contigs.fa|Edena_contigs.fa]], [[Media:SOAPdenovo contigs.fa|SOAPdenovo_contigs.fa]], [[Media:CLC contigs.fa|CLC_contigs.fa]], [[Media:Velvetcontigs.fa|Velvet_contigs.fa]]
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Statistics of the input assemblies:
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<blockquote>
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Abyss_contigs.fa
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<br>Number of contigs: 133
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<br>Length of the longest contig: 222425
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<br>whole:4626205
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<br>N50: 96511
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<br>Edena_contigs.fa
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<br>Number of contigs: 211
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<br>Length of the longest contig: 186686
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<br>whole:4569446
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<br>N50: 57790
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<br>SOAPdenovo_contigs.fa
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<br>Number of contigs: 553
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<br>Length of the longest contig: 103369
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<br>whole:4547211
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<br>N50: 17944
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<br>CLC_contigs.fa
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<br>Number of contigs: 378
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<br>Length of the longest contig: 107342
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<br>whole:4546827
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<br>N50: 29905
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<br>Velvet_contigs.fa
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<br>Number of contigs: 283
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<br>Length of the longest contig: 166094
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<br>whole:4550675
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<br>N50: 54359
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</blockquote>
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Output file: [[Media:Set1 Contigs.fa|Contigs.fa]]
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<ul><li><strong>Start to integrate contigs:</strong><br /></li></ul><blockquote><p>The content of the configuration file (CISA.config):</p></blockquote>
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<table width="457" border="1">
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<tr>
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<td height="152" align="left" bgcolor="#66CCFF">
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genome=4626205
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infile=Contigs.fa
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outfile=CISA.fa
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nucmer=path/nucmer
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R2_Gap=0.95
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CISA=path/CISA1.0
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makeblastdb=path/makeblastdb
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blastn=path/blastn
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</td>
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</tr>
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</table>
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<blockquote><p>The genome is set to 4626205 based on the genome size of Abyss.<br /></p></blockquote>
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<ul><li><strong>Command:</strong><br /></li></ul><blockquote><p>>python CISA.py CISA.config</p></blockquote>
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Input file: [[Media:Set1 Contigs.fa|Contigs.fa]]
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Output file: [[Media:CISA_Set1_Contigs.fa|CISA.fa]]
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