Guide
Examples
= Prerequisites = * Linux 64-bit environment [http://www.centos.org CentOS] * Python 2.X [http://www.python.org Python]<br> - Under centos: yum install python * MUMmer 3.22 or higher [http://mummer.sourceforge.net MUMmer] * Blast 2.2.25+ or higher [http://blast.ncbi.nlm.nih.gov Blast+] = Installation = Just to unpack the tar file.<br> Available commands: tar xvf CISA.tar. Execute access: chmod 755 -R CICA1.0 = Commands and configuration = <b><font size="5">Merge.py</font></b> Mergy.pu can convert data format to fit CISA. '''This is a essentail pre-work'''. Available commands: ./Merge.py myconfig The content of myconfig file: count=3 the number of dataset you would like to merge data=assembly1.fasta,title=Contig_m1 data=assembly2.fasta,title=Contig_m2 data=assembly3.fasta,title=Contig_m3 Master_file=Contigs_m.fa min_length=100 (default:100) Gap=11 min_length= It means that contig which is longer than 100 will be conserved. Gap= It's a optional variable.<br> if Gap attends, it will be used to split scoffolding by continuous 11 N.<br> if Gap is absent, the program will only merge data. If your data is from windows base. Please convert it to linux format. dos2unix Abyss_contigs.fa <b><font size="5">CISA.py</font></b> Available commands: ./CISA.py myconfig The content of myconfig genome=genome size infile=file outfile=file nucmer=path/nucmer Please modify the "path" into the 安裝路徑. R2_Gap=0.9 default:0.9 myconfig file中也改成0.9 CISA=path/CISA1.0 Please modify the "path" into the 安裝路徑. makeblastdb=path/makeblastdb Please modify the "path" into the 安裝路徑. blastn=path/blastn Please modify the "path" into the 安裝路徑. genome=<br> The genome size of each genome contain in genome_size.txt file. The largest genome size will be recommended to put here. We suggest to use the longest length which is between attended contigs as genome variable.<br> The break point of CISA will be set to 1.1 * genome variable. infile=<br> File name with input. outfile=<br> File name with output. nucmer=<br> Executive file for nucmer. If nucmer has beed set into the path, nucmer variable can be skipped. makeblastdb=<br> Executive file for makeblastdb. If makeblastdb has beed set into the path, makeblastdb variable can be skipped. blastn=<br> Executive file for blastn. If blastn has beed set into the path, blastn variable can be skipped. CISA=<br> Home directory of CISA. R2_Gap=<br> Tolerant amount of gap during CISA2 step. = Example = *'''Data Set:''' [[Ecoli|Ecoli]] *'''Merge Contigs:'''<br> The content of the configuration file:<br> ''count=5<br> data=Abyss_contigs.fa,title=Abyss<br> data=Edena_contigs.fa,title=Edena<br> data=SOAPdenovo_contigs.fa,title=SOAP<br> data=CLC_contigs.fa,title=CLC<br> data=Velvet_contigs.fa,title=Velvet<br> Master_file=Contigs.fa<br>'' Command:<br> ./Merge.py configuration_file *'''Start to integrate:'''<br> The content of the configuration file:<br> ''genome=4626205<br> infile=Contigs.fa<br> nucmer=path/nucmer<br> R2_Gap=0.95<br> CISA=path/CISA1.0<br> makeblastdb=path/makeblastdb<br> blastn=path/blastn<br>'' 4626205 which is the longest whole genome between different result from 5 assemblers is set into genome variable. Command:<br> ./CISA.py configuration_file
