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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 2.4.3 or higher
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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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Just only unpack the tar file.<br>
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Available commands:
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tar xvf CISA.tar.
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= Commands and configuration =
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<b><font size="5">Merge.py</font></b>
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Mergy.pu can convert data format to fit CISA. '''This is a essentail pre-work'''.
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Available commands:
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./Merge.py configuration_file
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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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The min_length means that contig which is longer than 100 will be conserved.
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The Gap is a optional variable.<br>
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if Gap attends, it will be used to split scoffolding by continuous 11 N.<br>
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if Gap is absent, the program will only merge data.
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<b><font size="5">CISA.py</font></b>
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Available commands:
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./CISA.py configuration_file
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The content of configuration file
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genome=genome size
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infile=Contigs.fa
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nucmer=path/nucmer
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R2_Gap=0.9 (default:0.9)
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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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genome
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We suggest to use the longest length which is between attended contigs as genome variable.<br>
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The break point of CISA will be set to 1.1 * genome variable.
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infile<br>
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File name with input.
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nucmer<br>
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Executive file for nucmer. If nucmer has beed set into the path, nucmer variable can be skipped.
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makeblastdb<br>
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Executive file for makeblastdb. If makeblastdb has beed set into the path, makeblastdb variable can be skipped.
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blastn<br>
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Executive file for blastn. If blastn has beed set into the path, blastn variable can be skipped.
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CISA<br>
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Home directory of CISA.
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R2_Gap<br>
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Tolerant amount of gap during CISA2 step.
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= Example =
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*'''Data Set:'''
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[[Ecoli|Ecoli]]
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*'''Merge Contigs:'''<br>
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The content of the configuration file:<br>
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''count=5<br>
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data=Abyss_contigs.fa,title=Abyss<br>
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data=Edena_contigs.fa,title=Edena<br>
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data=SOAPdenovo_contigs.fa,title=SOAP<br>
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data=CLC_contigs.fa,title=CLC<br>
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data=Velvet_contigs.fa,title=Velvet<br>
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Master_file=Contigs.fa<br>''
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Command:<br>
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./Merge.py configuration_file
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*'''Start to integrate:'''<br>
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The content of the configuration file:<br>
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''genome=4626205<br>
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infile=Contigs.fa<br>
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nucmer=path/nucmer<br>
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R2_Gap=0.95<br>
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CISA=path/CISA1.0<br>
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makeblastdb=path/makeblastdb<br>
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blastn=path/blastn<br>''
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4626205 which is the longest whole genome between different result from 5 assemblers is set into genome variable.
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Command:<br>
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./CISA.py configuration_file
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