Guide
Examples
== Prerequisites == Linux 64-bit environment http://www.centos.org Python 2.4.3 or higher http://www.python.org/ - Under centos: yum install python MUMmer 3.22 or higher http://mummer.sourceforge.net/ Blast 2.2.25+ or higher http://blast.ncbi.nlm.nih.gov/ == 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 File name with input. nucmer Executive file for nucmer. If nucmer has beed set into the path, nucmer can be skipped. makeblastdb Executive file for makeblastdb. If makeblastdb has beed set into the path, makeblastdb can be skipped. blastn Executive file for blastn. If blastn has beed set into the path, blastn can be skipped. CISA Home directory for CISA. R2_Gap Tolerant amount of gap during CISA2.
