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.
