Guide
Examples
= Prerequisites = * Linux 64-bit environment http://www.centos.org [http://www.centos.org CentOS] * Python 2.4.3 or higher http://www.python.org [http://www.python.org Python] - Under centos: yum install python * MUMmer 3.22 or higher http://mummer.sourceforge.net [http://mummer.sourceforge.net MUMmer] * Blast 2.2.25+ or higher http://blast.ncbi.nlm.nih.gov [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=119169466 infile=Contigs.fa nucmer=/opt/MUMmer3.22/nucmer R2_Gap=0.95 CISA=../SoftWare/CISA1.0 makeblastdb=makeblastdb blastn=blastn genome We suggest to use the longest length which is between attended contigs as genome. The break point of CISA depends on it. infile<br> File name with input. nucmer<br> Executive file for nucmer. If nucmer has beed set into the path, nucmer can be skipped. makeblastdb<br> Executive file for makeblastdb. If makeblastdb has beed set into the path, makeblastdb can be skipped. blastn<br> Executive file for blastn. If blastn has beed set into the path, blastn can be skipped. CISA<br> Home directory for CISA. R2_Gap<br> Tolerant amount of gap during CISA2. = Example = [[Ecoli|Ecoli]]
