Guide
Examples
= Prerequisites = * Linux 64-bit environment [http://www.centos.org CentOS] * Python 2.4.3 or higher [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 = = Commands and configuration = <b><font size="5">Merge.py</font></b> Available commands: ./Merge.py configuration_file The content of configuration file: count=3 data=assembly1.fasta,title=Contig_m1 data=assembly2.fasta,title=Contig_m2 data=assembly3.fasta,title=Contig_m3 Master_file=Contigs_m.fa Gap=11 if 'Gap' attends, it will be used to split scoffolding by continuous 11 N. if 'Gap' is absent, the program will only merge data. <b><font size="5">CISA.py</font></b> Available commands: ./CISA.py configuration_file The content of configuration file genome=break point infile=Contigs.fa nucmer=path/nucmer R2_Gap=0.9 (default:0.9) CISA=path/CISA1.0 makeblastdb=path/makeblastdb blastn=path/blastn genome We suggest to use the longest length which is between attended contigs as genome variable.<br> The break point of CISA will be set with 1.1 * genome variable. infile<br> File name with input. 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 = [[Ecoli|Ecoli]]
